Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold793
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: 691781
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 4 of 5
Found at i:448802 original size:13 final size:13
Alignment explanation
Indices: 448784--448809 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
448774 TATAGCAAGT
448784 ATGTATCGATACA
1 ATGTATCGATACA
448797 ATGTATCGATACA
1 ATGTATCGATACA
448810 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:452018 original size:19 final size:19
Alignment explanation
Indices: 451994--452088 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
451984 CAACGATTTG
451994 TATCGATACATAAGTGTTA
1 TATCGATACATAAGTGTTA
452013 TATCGATAC--AA-TG-TA
1 TATCGATACATAAGTGTTA
*
452028 T-T-GATACATAAGTGTTG
1 TATCGATACATAAGTGTTA
452045 TATCGATAC--AA-TG---
1 TATCGATACATAAGTGTTA
*
452058 TATCGATACATAAGTGTTG
1 TATCGATACATAAGTGTTA
452077 TATCGATACATA
1 TATCGATACATA
452089 TGAAGCTACT
Statistics
Matches: 63, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 14 0.22
14 1 0.02
15 7 0.11
16 8 0.13
17 6 0.10
18 1 0.02
19 26 0.41
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (19 bp):
TATCGATACATAAGTGTTA
Found at i:452028 original size:32 final size:32
Alignment explanation
Indices: 451992--452086 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
451982 TTCAACGATT
*
451992 TGTATCGATACATAAGTGTTATATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
452024 TGTATTGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
452056 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
452087 TATGAAGCTA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:452061 original size:13 final size:13
Alignment explanation
Indices: 452043--452067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
452033 ACATAAGTGT
452043 TGTATCGATACAA
1 TGTATCGATACAA
452056 TGTATCGATACA
1 TGTATCGATACA
452068 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:452266 original size:52 final size:51
Alignment explanation
Indices: 452163--452290 Score: 195
Period size: 52 Copynumber: 2.5 Consensus size: 51
452153 CACTGATCTT
*
452163 TGTATCGATACATGA-AGCCAAATTTGCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACAT-ACAGGCAAATTTGCCAGATGTATCGATACACTATGAAA
*
452214 TGTATCGATACATACAGGCAAATTTGCCTGGATGTATCGATACACTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCC-AGATGTATCGATACACTATGAAA
* *
452266 TGTATCGATACATGCAGGCAGATTT
1 TGTATCGATACATACAGGCAAATTT
452291 TCATATTTCG
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
50 1 0.01
51 25 0.35
52 45 0.63
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATACAGGCAAATTTGCCAGATGTATCGATACACTATGAAA
Found at i:459962 original size:13 final size:13
Alignment explanation
Indices: 459944--459973 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
459934 ACTTTTCACC
459944 ATGTATCGATACA
1 ATGTATCGATACA
459957 ATGTATCGATACA
1 ATGTATCGATACA
459970 ATGT
1 ATGT
459974 CCCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:459965 original size:33 final size:33
Alignment explanation
Indices: 459923--459990 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
459913 CGTTGGGCAT
* *
459923 AATGTATCGATAC-TTTTCACCATGTATCGATAC
1 AATGTATCGATACAATGTC-CCATGTATCGATAC
459956 AATGTATCGATACAATGTCCCATGTATCGATAC
1 AATGTATCGATACAATGTCCCATGTATCGATAC
459989 AA
1 AA
459991 ATAGTGGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.91
34 3 0.09
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (33 bp):
AATGTATCGATACAATGTCCCATGTATCGATAC
Found at i:474478 original size:8 final size:8
Alignment explanation
Indices: 474465--474490 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
474455 ATTTGATTAA
474465 ATTTTGTG
1 ATTTTGTG
474473 ATTTTGTG
1 ATTTTGTG
474481 ATTTTGTG
1 ATTTTGTG
474489 AT
1 AT
474491 GAATGATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (8 bp):
ATTTTGTG
Found at i:475167 original size:21 final size:21
Alignment explanation
Indices: 475126--475168 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
475116 CCTCTAGGCA
*
475126 GCACTCACCAGGTCGCGACCG
1 GCACTCACCAGGTCGCAACCG
*
475147 GCACTCACCAGGTCGTAACCG
1 GCACTCACCAGGTCGCAACCG
475168 G
1 G
475169 GCAACCCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.40, G:0.28, T:0.12
Consensus pattern (21 bp):
GCACTCACCAGGTCGCAACCG
Found at i:476569 original size:22 final size:21
Alignment explanation
Indices: 476543--476586 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
476533 CGAAATTGTT
*
476543 AAATTATTTTACTAAGGGGGAG
1 AAATT-TTTGACTAAGGGGGAG
*
476565 AAATTTTTGATTAAGGGGGAG
1 AAATTTTTGACTAAGGGGGAG
476586 A
1 A
476587 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.32
Consensus pattern (21 bp):
AAATTTTTGACTAAGGGGGAG
Found at i:480368 original size:20 final size:20
Alignment explanation
Indices: 480343--480417 Score: 114
Period size: 20 Copynumber: 3.8 Consensus size: 20
480333 TTTTACCTAG
*
480343 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
480363 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
480383 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
480403 ATGTATCGATACATT
1 ATGTATCGATACATT
480418 CTATTTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:481310 original size:21 final size:20
Alignment explanation
Indices: 481280--481326 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
481270 CTAAATAACT
481280 CATGTCCATGCATTTTAAGC
1 CATGTCCATGCATTTTAAGC
481300 CATGTACCATGCATTTTAA--
1 CATGT-CCATGCATTTTAAGC
481319 CATGTCCA
1 CATGTCCA
481327 ACATCTAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.12
19 5 0.19
20 5 0.19
21 13 0.50
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.34
Consensus pattern (20 bp):
CATGTCCATGCATTTTAAGC
Found at i:497035 original size:19 final size:20
Alignment explanation
Indices: 496991--497061 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
496981 CTACCAGTTT
* * *
496991 CATGTATCGATATAATTATG
1 CATGTATCGATACAATGATA
497011 CATGTATCGATACAATGA-A
1 CATGTATCGATACAATGATA
*
497030 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-ATA
497051 -ATGTATCGATA
1 CATGTATCGATA
497062 AATCTGGATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.36
20 28 0.62
21 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATGATA
Found at i:497056 original size:20 final size:19
Alignment explanation
Indices: 497011--497061 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
497001 TATAATTATG
*
497011 CATGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
497030 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAG-A-A
497051 -ATGTATCGATA
1 CATGTATCGATA
497062 AATCTGGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 16 0.55
20 12 0.41
21 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:497444 original size:20 final size:21
Alignment explanation
Indices: 497395--497448 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
497385 ACAATGAGAA
497395 ATGTATCGATACATTGCAAGC
1 ATGTATCGATACATTGCAAGC
* ***
497416 ATGTTTCGATACATT-CACTT
1 ATGTATCGATACATTGCAAGC
497436 ATGTATCGATACA
1 ATGTATCGATACA
497449 ATTTCTTTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTGCAAGC
Found at i:498302 original size:157 final size:156
Alignment explanation
Indices: 497850--498489 Score: 630
Period size: 156 Copynumber: 4.1 Consensus size: 156
497840 GTGTCTAAAA
* * * * * * * ** * *
497850 TTATAGATGGGATGAACCTA-CCTAAATACCTACCTTCGGCATAAAAGTAGACCTGGTAACAACT
1 TTATAGCTGGGGTGAACCTATCCTAAATACCCACATTTGGCATAAAAGCAAACCAAGTGACAACC
* * * ** ** ** * * *
497914 TAGAACTCGATTCTAGAAAATTACGACGATGCTTCTATA-GTATACCTTGGACATTAAAGTATTT
66 TAGGACTCGGTTCTAAAAAATTATAAAAATGCCCCTATAGGTATACCTTCGACATGAAAGTTTTT
*
497978 CAGTAATCCTAAATG-ACTTAAAAAGG
131 CAGTAACCCTAAA-GAACTTAAAAAGG
* * * * * * * *
498004 TTATAGTTTGGGTGAACATATCCTAAATACCCACCTTCGGCAAAAAAGTAAACCCAA-TAACAAC
1 TTATAGCTGGGGTGAACCTATCCTAAATACCCACATTTGGCATAAAAGCAAA-CCAAGTGACAAC
** * * *
498068 CTAGGACTCGGTTCTAAAAAATTACGAAAATGCCCATATAGGTATACCTTCGACAAGAAAG--TA
65 CTAGGACTCGGTTCTAAAAAATTATAAAAATGCCCCTATAGGTATACCTTCGACATGAAAGTTTT
*
498131 TCATGGTAATCCTAAAGAACTTAAAAAGG
130 TCA--GTAACCCTAAAGAACTTAAAAAGG
498160 TTATAGCTGGGGTGAACCTATCCTAAATACCC-CATTTGGCATAAAAGCAAACCAAGTGACAACC
1 TTATAGCTGGGGTGAACCTATCCTAAATACCCACATTTGGCATAAAAGCAAACCAAGTGACAACC
** *
498224 TAGGACTTAGTTCTAGAAAAAATTATAAAAATGCCCCTATAGGTATACCTTTGACATGAAAGTTT
66 TAGGACTCGGTTCT--AAAAAATTATAAAAATGCCCCTATAGGTATACCTTCGACATGAAAGTTT
* *
498289 TTCGGTAACCCTAAAGGACTTAAAAAGG
129 TTCAGTAACCCTAAAGAACTTAAAAAGG
* * * * * * *** * *
498317 GTATAGTTGGGATGAACCTATCCTAAATACCCACTTTTAGCATAAAAGCAGACTGGGTGAAAACT
1 TTATAGCTGGGGTGAACCTATCCTAAATACCCACATTTGGCATAAAAGCAAACCAAGTGACAACC
* * * *
498382 TAGGACTCGGTTCTAAAAAATTATAAAAATACTCCTATAGGTATACCTTCAACATGAAAATTTTT
66 TAGGACTCGGTTCTAAAAAATTATAAAAATGCCCCTATAGGTATACCTTCGACATGAAAGTTTTT
498447 CAGTAACCCTAAA-AGACTTAAAAAGG
131 CAGTAACCCTAAAGA-ACTTAAAAAGG
*
498473 TTATAGCTAGGGTGAAC
1 TTATAGCTGGGGTGAAC
498490 TACCTACCTT
Statistics
Matches: 408, Mismatches: 65, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
154 24 0.06
155 101 0.25
156 152 0.37
157 92 0.23
158 36 0.09
159 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (156 bp):
TTATAGCTGGGGTGAACCTATCCTAAATACCCACATTTGGCATAAAAGCAAACCAAGTGACAACC
TAGGACTCGGTTCTAAAAAATTATAAAAATGCCCCTATAGGTATACCTTCGACATGAAAGTTTTT
CAGTAACCCTAAAGAACTTAAAAAGG
Found at i:502043 original size:20 final size:20
Alignment explanation
Indices: 502018--502055 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
502008 GGGTTTTCTA
502018 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
502038 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
502056 GGAAAATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:502879 original size:19 final size:20
Alignment explanation
Indices: 502855--502905 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
502845 TAGCTAAACT
**
502855 TGTATCGATACA-CATAGTA
1 TGTATCGATACACCATAAAA
502874 TGTATCGATACACCATAAAA
1 TGTATCGATACACCATAAAA
502894 TGTATCGATACA
1 TGTATCGATACA
502906 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (20 bp):
TGTATCGATACACCATAAAA
Found at i:508374 original size:20 final size:20
Alignment explanation
Indices: 508348--508422 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
508338 TTCCCGTAGC
*
508348 CATGTATCAATACAATACATA
1 CATGTATCGATACAATACA-A
*
508369 -ATGTATCGATACAATTCAA
1 CATGTATCGATACAATACAA
** *
508388 CATGTATCGATACAATGTAC
1 CATGTATCGATACAATACAA
508408 CATGTATCGATACAA
1 CATGTATCGATACAA
508423 ACAGTGGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.02
20 47 0.98
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATACAA
Found at i:508510 original size:13 final size:13
Alignment explanation
Indices: 508492--508518 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
508482 TACAATGAAC
508492 ATGTATCGATACA
1 ATGTATCGATACA
508505 ATGTATCGATACA
1 ATGTATCGATACA
508518 A
1 A
508519 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:508514 original size:32 final size:33
Alignment explanation
Indices: 508473--508536 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
508463 CAAATTGTCC
*
508473 ATGTATCGATACAATG-A-ACATGTATCGATACA
1 ATGTATCGATACAAAGCATA-ATGTATCGATACA
508505 ATGTATCGATACAAAGCATAATGTATCGATAC
1 ATGTATCGATACAAAGCATAATGTATCGATAC
508537 CTCTGGGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 13 0.45
34 1 0.03
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATACA
Found at i:509128 original size:150 final size:153
Alignment explanation
Indices: 508826--509175 Score: 406
Period size: 150 Copynumber: 2.3 Consensus size: 153
508816 AGATCCTAAC
* * * * * **
508826 ACCTTCAATAAGAAAGTTTCCCAGTAACCCTAAAGGACTTAAAACAGTTATAGTTGGGATGAATG
1 ACCTTCAACATGAAAGTAT-CCAGTAACCCTAAAGGACATAAAACAGGTATAG-TGGGATGAACC
* * * *
508891 TATCCTCAATACCTACCTTCGGCATAAAAGTGGGCCCGATGACAACCTAGGACTCAGTTCTAAAA
64 TATCCTAAATACCCACCTTCGGCATAAAAGCGGGCCCGATGACAACCTAAGACTCAGTTCTAAAA
*
508956 AAATACAAAAATATCCCAATGGGTAT
129 AAATACAAAAATA-CCCAATGGGCAT
* ***
508982 ACCTTCAACATGAAAGTTTTTGGTAACCCTAAAGGACATAAAA-AGGT-TA-T-GGATGAACCTA
1 ACCTTCAACATGAAAGTATCCAGTAACCCTAAAGGACATAAAACAGGTATAGTGGGATGAACCTA
*
509043 TCCTAAATACCCACCTTCGGCATAAAAGCGGGCCCGATGATAACCTAAGACTC-GATTCTAAAAA
66 TCCTAAATACCCACCTTCGGCATAAAAGCGGGCCCGATGACAACCTAAGACTCAG-TTCTAAAAA
*
509107 ATTACAAAAATA-CCATTATGGGCAT
130 AATACAAAAATACCCA--ATGGGCAT
* * *
509132 ACCTTCGACGTGAAAGTATCCAGTAACCCTAATGGACACTAAAA
1 ACCTTCAACATGAAAGTATCCAGTAACCCTAAAGGACA-TAAAA
509176 TGATAAACAA
Statistics
Matches: 167, Mismatches: 23, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
148 3 0.02
149 1 0.01
150 115 0.69
151 6 0.04
153 2 0.01
154 3 0.02
155 20 0.12
156 17 0.10
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (153 bp):
ACCTTCAACATGAAAGTATCCAGTAACCCTAAAGGACATAAAACAGGTATAGTGGGATGAACCTA
TCCTAAATACCCACCTTCGGCATAAAAGCGGGCCCGATGACAACCTAAGACTCAGTTCTAAAAAA
ATACAAAAATACCCAATGGGCAT
Found at i:510952 original size:20 final size:20
Alignment explanation
Indices: 510927--511022 Score: 87
Period size: 20 Copynumber: 5.0 Consensus size: 20
510917 GAAAGTTATG
*
510927 AAAGCATGAAACGATGATGC
1 AAAGCATGAAATGATGATGC
*
510947 AAAGCATGTAATG-TGGATGC
1 AAAGCATGAAATGAT-GATGC
*
510967 -AAGTATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
* *
510986 AAAGCATG--GTGGTTG-TG-
1 AAAGCATGAAAT-GATGATGC
511003 AAAGCATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
511023 CATGTAACGT
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
17 8 0.14
18 6 0.10
19 22 0.37
20 23 0.39
ACGTcount: A:0.39, C:0.09, G:0.29, T:0.23
Consensus pattern (20 bp):
AAAGCATGAAATGATGATGC
Found at i:510984 original size:19 final size:19
Alignment explanation
Indices: 510928--511022 Score: 72
Period size: 19 Copynumber: 5.0 Consensus size: 19
510918 AAAGTTATGA
*
510928 AAGCATGAAACGATGATGC
1 AAGCATGAAATGATGATGC
*
510947 AAAGCATGTAATG-TGGATGC
1 -AAGCATGAAATGAT-GATGC
*
510967 AAGTATGAAATGATGATGC
1 AAGCATGAAATGATGATGC
* * *
510986 AAAGCATG--GTGGTTG-TGA
1 -AAGCATGAAAT-GATGATGC
511004 AAGCATGAAATGATGATGC
1 AAGCATGAAATGATGATGC
511023 CATGTAACGT
Statistics
Matches: 57, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
17 7 0.12
18 6 0.11
19 22 0.39
20 22 0.39
ACGTcount: A:0.38, C:0.09, G:0.29, T:0.23
Consensus pattern (19 bp):
AAGCATGAAATGATGATGC
Found at i:511768 original size:20 final size:20
Alignment explanation
Indices: 511731--511768 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
511721 TGATTTTATT
*
511731 TATATATTTGTTTGTTTGTG
1 TATATATTTGTTTATTTGTG
511751 TATAT-TTTGATTTATTTG
1 TATATATTTG-TTTATTTG
511769 AAAATCTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.18, C:0.00, G:0.16, T:0.66
Consensus pattern (20 bp):
TATATATTTGTTTATTTGTG
Found at i:516930 original size:22 final size:21
Alignment explanation
Indices: 516871--516930 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
516861 TAGCTTAATT
*
516871 GCATTCATCATTATTTTCATG
1 GCATTCATCATTATTTTCATA
* *
516892 GCATTAATACATCATTTTCATAA
1 GCATTCAT-CATTATTTTCAT-A
*
516915 TCATTCATCATTATTT
1 GCATTCATCATTATTT
516931 GCTTAATTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 7 0.23
22 18 0.58
23 6 0.19
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (21 bp):
GCATTCATCATTATTTTCATA
Found at i:525441 original size:42 final size:42
Alignment explanation
Indices: 525395--526094 Score: 389
Period size: 42 Copynumber: 16.6 Consensus size: 42
525385 AATCTGCCTA
* *
525395 TCGGCTTTGACCCTAGAGA-TTGCCTCATCTAAGGTCTGCTTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCATCTAA-GTCTGCTTG
* * *
525437 TCGGCTTTGACCCTGAAGACTTTCCT-ATCCTTCAGTCTGCCTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCAT-C-TAAGTCTGCTTG
* * * * * *
525480 TTGGCTTTGACCTTAGAGAC-TGCCTCATTTAAAATCTGCTTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCATCT-AAGTCTGCTTG
* * * * * *
525522 TCGGCTTTGACCTTGGAGACTTT-CTTATCCTTCAGTTTGCCTA
1 TCGGCTTTGACCCTGGAGACTTTCCTCAT-C-TAAGTCTGCTTG
* * * *
525565 TCGGCTTTGACCTTGGAGACTTTTCT-ACCCTCAGTCTGCTTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCA-TCTAAGTCTGCTTG
*
525607 TTGGCTTTGACCCTGGAGAC-TTCCTCATCTAAGGTCTGCTTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCATCTAA-GTCTGCTTG
* * * *
525649 TCGGCTTTGACCTTAGAGACTTTCCT-ACCTTCAA-TCTGCCTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCATC-T-AAGTCTGCTTG
* * * * *
525691 TCAGCTTTGACCCTAGAGAC-TACCTCATCTAAAGTCTACCTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCATCT-AAGTCTGCTTG
* * * * * *
525733 TTGG-TTTGAGCTTGGAGACTTTTCT-ACCCTCAA-TCTACTTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCA-TCT-AAGTCTGCTTG
* * * *
525774 TCGACTTTGACCTTGGAGAC-TGCCTCATCTAAAGTCTGCTTC
1 TCGGCTTTGACCCTGGAGACTTTCCTCATCT-AAGTCTGCTTG
** * * * *
525816 TCGGCTTTGACCCTACAGACTTTTCT-ACCCTCAGTCTGCCTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCA-TCTAAGTCTGCTTG
* * * * * *
525858 TCGACTGTGACCCTGGAGAC-TGCCTCATCTAAAGCCTACCTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCATCT-AAGTCTGCTTG
* * *
525900 TCGACCTTGACCCTGGAGACTTTCCT-ATCCTTCAA-TCTGCGTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCAT-C-T-AAGTCTGCTTG
* * * * *
525943 TTGGCTTTGACCCTAGAGAC-TGCCTCATTTAAAGTTTG-TCTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCATCT-AAGTCTGCT-TG
* * * *
525985 TCGGCTTTAACCTTGGAGACTTTCCT-ATCCTTCAGTCTGCCTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCAT-C-TAAGTCTGCTTG
* * * *
526028 TCGACTTTGACCTTGGAGACTTT-CTTATCCTTTAGTCTGCTTG
1 TCGGCTTTGACCCTGGAGACTTTCCTCAT-C-TAAGTCTGCTTG
* *
526071 TTGGCTTTGACCCTGGAGAATTTC
1 TCGGCTTTGACCCTGGAGACTTTC
526095 ATCCGGGTCC
Statistics
Matches: 504, Mismatches: 116, Indels: 74
0.73 0.17 0.11
Matches are distributed among these distances:
41 52 0.10
42 272 0.54
43 169 0.34
44 11 0.02
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.36
Consensus pattern (42 bp):
TCGGCTTTGACCCTGGAGACTTTCCTCATCTAAGTCTGCTTG
Found at i:525476 original size:85 final size:84
Alignment explanation
Indices: 525332--525667 Score: 322
Period size: 85 Copynumber: 4.0 Consensus size: 84
525322 CTTTAGTCTA
* * * * * *
525332 CCTCATTTAAAGTCTGCCTATCAGCTTTGACCTTAGAA-ACTTTCCTATCTTCCAATCTGCCTAT
1 CCTCATCTAAAGTCTGCTTGTCGGCTTTGACCCT-GAAGACTTTCCTATCTT-CAGTCTGCCTAT
*
525396 CGGCTTTGACCCTAGAGATTG
64 CGGCTTTGACCTTAGAGATTG
* * *
525417 CCTCATCTAAGGTCTGCTTGTCGGCTTTGACCCTGAAGACTTTCCTATCCTTCAGTCTGCCTGTT
1 CCTCATCTAAAGTCTGCTTGTCGGCTTTGACCCTGAAGACTTTCCTAT-CTTCAGTCTGCCTATC
*
525482 GGCTTTGACCTTAGAGACTG
65 GGCTTTGACCTTAGAGATTG
* * * * * *
525502 CCTCATTTAAAATCTGCTTGTCGGCTTTGACCTTGGAGACTTTCTTATCCTTCAGTTTGCCTATC
1 CCTCATCTAAAGTCTGCTTGTCGGCTTTGACCCTGAAGACTTTCCTAT-CTTCAGTCTGCCTATC
* *
525567 GGCTTTGACCTTGGAGACTTT
65 GGCTTTGACCTTAGAGA-TTG
* * * * * * * *
525588 TCT-ACCCT-CAGTCTGCTTGTTGGCTTTGACCCTGGAGAC-TTCCTCATC-TAAGGTCTGCTTG
1 CCTCA-TCTAAAGTCTGCTTGTCGGCTTTGACCCTGAAGACTTTCCT-ATCTTCA-GTCTGCCTA
525649 TCGGCTTTGACCTTAGAGA
63 TCGGCTTTGACCTTAGAGA
525668 CTTTCCTACC
Statistics
Matches: 209, Mismatches: 36, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
83 2 0.01
84 32 0.15
85 168 0.80
86 7 0.03
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (84 bp):
CCTCATCTAAAGTCTGCTTGTCGGCTTTGACCCTGAAGACTTTCCTATCTTCAGTCTGCCTATCG
GCTTTGACCTTAGAGATTG
Found at i:525609 original size:127 final size:127
Alignment explanation
Indices: 525437--525963 Score: 417
Period size: 127 Copynumber: 4.2 Consensus size: 127
525427 GGTCTGCTTG
* * *
525437 TCGGCTTTGACCCTGAAGACTTTCCTATCCTTCAGTCTGCCTGTTGGCTTTGACCTTAGAGACTG
1 TCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTTGGCTTTGACCCTAGAGACTG
* * * * *
525502 CCTCATTTAAAATCTGCTTGTCGGCTTTGACCTTGGAGACTTTCTTATCCTTCAGTTTGCCTA
66 CCTCATCTAAAATCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTA-CCTTCAATCTGCCTA
* * * * *
525565 TCGGCTTTGACCTTGGAGACTTTTCTA-CCCTCAGTCTGCTTGTTGGCTTTGACCCTGGAGACTT
1 TCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTTGGCTTTGACCCTAGAGACTG
** *
525629 CCTCATCTAAGGTCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTACCTTCAATCTGCCTG
66 CCTCATCTAAAATCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTACCTTCAATCTGCCTA
* * * * * * * *
525691 TCAGCTTTGACCCTAGAGAC-TACCTCAT--CTAAAGTCTACCTGTTGG-TTTGAGCTTGGAGAC
1 TCGGCTTTGACCCTGGAGACTTTCCT-ATCCCT-CAGTCTGCCTGTTGGCTTTGACCCTAGAGAC
** * * * * * * * *
525752 T-TTTCTACCCT-CAATCTACTTGTCGACTTTGACCTTGGAGAC-TGCCT-CATCTAAAGTCTGC
64 TGCCTC-A-TCTAAAATCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTACCT-TCAA-TCTGC
* *
525813 TTC
125 CTA
** * * * * *
525816 TCGGCTTTGACCCTACAGACTTTTCTA-CCCTCAGTCTGCCTGTCGACTGTGACCCTGGAGACTG
1 TCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTTGGCTTTGACCCTAGAGACTG
** * * * * * * * *
525880 CCTCATCTAAAGCCTACCTGTCGACCTTGACCCTGGAGACTTTCCTATCCTTCAATCTGCGTG
66 CCTCATCTAAAATCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTA-CCTTCAATCTGCCTA
* *
525943 TTGGCTTTGACCCTAGAGACT
1 TCGGCTTTGACCCTGGAGACT
525964 GCCTCATTTA
Statistics
Matches: 316, Mismatches: 67, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
123 2 0.01
124 9 0.03
125 83 0.26
126 88 0.28
127 105 0.33
128 27 0.09
129 2 0.01
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (127 bp):
TCGGCTTTGACCCTGGAGACTTTCCTATCCCTCAGTCTGCCTGTTGGCTTTGACCCTAGAGACTG
CCTCATCTAAAATCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTACCTTCAATCTGCCTA
Found at i:525687 original size:84 final size:84
Alignment explanation
Indices: 525429--526094 Score: 584
Period size: 85 Copynumber: 7.9 Consensus size: 84
525419 TCATCTAAGG
* ** *
525429 TCTGCTTGTCGGCTTTGACCCTGAAGACTTTCCT-ATCCTTCAGTCTGCCTGTTGGCTTTGACCT
1 TCTGCTTGTCGGCTTTGACCCTGGAGAC-TTCCTCAT-CTAAAGTCTGCCTGTCGGCTTTGACCT
* * * *
525493 TAGAGAC-TGCCT-CATTTAAAA
64 TGGAGACTTTCCTAC-CTT-CAA
* * * ** * *
525514 TCTGCTTGTCGGCTTTGACCTTGGAGACTTTCTTATCCTTCAGTTTGCCTATCGGCTTTGACCTT
1 TCTGCTTGTCGGCTTTGACCCTGGAGACTTCCTCAT-CTAAAGTCTGCCTGTCGGCTTTGACCTT
* * *
525579 GGAGACTTTTCTACCCTCAG
65 GGAGACTTTCCTACCTTCAA
* * * *
525599 TCTGCTTGTTGGCTTTGACCCTGGAGACTTCCTCATCTAAGGTCTGCTTGTCGGCTTTGACCTTA
1 TCTGCTTGTCGGCTTTGACCCTGGAGACTTCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTG
525664 GAGACTTTCCTACCTTCAA
66 GAGACTTTCCTACCTTCAA
* * * * * * *
525683 TCTGCCTGTCAGCTTTGACCCTAGAGACTACCTCATCTAAAGTCTACCTGTTGG-TTTGAGCTTG
1 TCTGCTTGTCGGCTTTGACCCTGGAGACTTCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTG
* *
525747 GAGACTTTTCTACCCTCAA
66 GAGACTTTCCTACCTTCAA
* * * * * * * *
525766 TCTACTTGTCGACTTTGACCTTGGAGACTGCCTCATCTAAAGTCTGCTTCTCGGCTTTGACCCTA
1 TCTGCTTGTCGGCTTTGACCCTGGAGACTTCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTG
* * * *
525831 CAGACTTTTCTACCCTCAG
66 GAGACTTTCCTACCTTCAA
* * * * * * * * *
525850 TCTGCCTGTCGACTGTGACCCTGGAGACTGCCTCATCTAAAGCCTACCTGTCGACCTTGACCCTG
1 TCTGCTTGTCGGCTTTGACCCTGGAGACTTCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTG
525915 GAGACTTTCCTATCCTTCAA
66 GAGACTTTCCTA-CCTTCAA
* * * * * * * *
525935 TCTGCGTGTTGGCTTTGACCCTAGAGACTGCCTCATTTAAAGTTTGTCTGTCGGCTTTAACCTTG
1 TCTGCTTGTCGGCTTTGACCCTGGAGACTTCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTG
*
526000 GAGACTTTCCTATCCTTCAG
66 GAGACTTTCCTA-CCTTCAA
* * * * * ** * * *
526020 TCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTATCCTTTAGTCTGCTTGTTGGCTTTGACCCT
1 TCTGCTTGTCGGCTTTGACCCTGGAGACTTCCTCAT-CTAAAGTCTGCCTGTCGGCTTTGACCTT
*
526085 GGAGAATTTC
65 GGAGACTTTC
526095 ATCCGGGTCC
Statistics
Matches: 471, Mismatches: 104, Indels: 11
0.80 0.18 0.02
Matches are distributed among these distances:
83 68 0.14
84 175 0.37
85 195 0.41
86 32 0.07
87 1 0.00
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (84 bp):
TCTGCTTGTCGGCTTTGACCCTGGAGACTTCCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTG
GAGACTTTCCTACCTTCAA
Found at i:525793 original size:167 final size:168
Alignment explanation
Indices: 525569--526048 Score: 624
Period size: 167 Copynumber: 2.9 Consensus size: 168
525559 TGCCTATCGG
* *
525569 CTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCTTGTTGGCTTTGACCCTGGAGACTTCCTCA
1 CTTTGACCTTGGAGACTTTTCTACCCTCAATCTGCTTGTTGGCTTTGACCCTGGAGACTGCCTCA
* *
525634 TCTAAGGTCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTACCTTCAATCTGCCTGTC-AGCTT
66 TCTAAAGTCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGA-CTT
* * *
525698 TGACCCTAGAGACTACCTCATCTAAAGTCTACCTGTTG-
130 TGACCCTGGAGACTACCTCATCTAAAGCCTACCTGTCGA
* * * * * *
525736 GTTTGAGCTTGGAGACTTTTCTACCCTCAATCTACTTGTCGACTTTGACCTTGGAGACTGCCTCA
1 CTTTGACCTTGGAGACTTTTCTACCCTCAATCTGCTTGTTGGCTTTGACCCTGGAGACTGCCTCA
* * * * * *
525801 TCTAAAGTCTGCTTCTCGGCTTTGACCCTACAGACTTTTCTACCCTCAGTCTGCCTGTCGACTGT
66 TCTAAAGTCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGACTTT
*
525866 GACCCTGGAGACTGCCTCATCTAAAGCCTACCTGTCGA
131 GACCCTGGAGACTACCTCATCTAAAGCCTACCTGTCGA
* * * * * *
525904 CCTTGACCCTGGAGACTTTCCTATCCTTCAATCTGCGTGTTGGCTTTGACCCTAGAGACTGCCTC
1 CTTTGACCTTGGAGACTTTTCTA-CCCTCAATCTGCTTGTTGGCTTTGACCCTGGAGACTGCCTC
* * * *
525969 ATTTAAAGTTTG-TCTGTCGGCTTTAACCTTGGAGACTTTCCTATCCTTCAGTCTGCCTGTCGAC
65 ATCTAAAGTCTGCT-TGTCGGCTTTGACCTTAGAGACTTTCCTA-CCTTCAGTCTGCCTGTCGAC
*
526033 TTTGACCTTGGAGACT
128 TTTGACCCTGGAGACT
526049 TTCTTATCCT
Statistics
Matches: 265, Mismatches: 43, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
167 145 0.55
168 20 0.08
169 67 0.25
170 33 0.12
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.34
Consensus pattern (168 bp):
CTTTGACCTTGGAGACTTTTCTACCCTCAATCTGCTTGTTGGCTTTGACCCTGGAGACTGCCTCA
TCTAAAGTCTGCTTGTCGGCTTTGACCTTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGACTTT
GACCCTGGAGACTACCTCATCTAAAGCCTACCTGTCGA
Found at i:526414 original size:20 final size:19
Alignment explanation
Indices: 526365--526428 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
526355 GATAAAAATT
*
526365 AAAAATCAAGAA-ATTAAAA
1 AAAAATCAA-AATAATAAAA
*
526384 AAATAA-AAAAATCAATAAAA
1 AAA-AATCAAAAT-AATAAAA
* *
526404 AAAAATCAAAATTATCAAA
1 AAAAATCAAAATAATAAAA
526423 AAAAAT
1 AAAAAT
526429 GATGAATGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 2 0.06
19 18 0.50
20 16 0.44
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (19 bp):
AAAAATCAAAATAATAAAA
Found at i:526414 original size:23 final size:21
Alignment explanation
Indices: 526380--526427 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
526370 TCAAGAAATT
526380 AAAAAAATAAAAAAATCAATAA
1 AAAAAAATAAAAAAATCAA-AA
**
526402 AAAAAAATCAAAATTATCAAAA
1 AAAAAAAT-AAAAAAATCAAAA
526424 AAAA
1 AAAA
526428 TGATGAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (21 bp):
AAAAAAATAAAAAAATCAAAA
Found at i:526521 original size:23 final size:23
Alignment explanation
Indices: 526494--526539 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
526484 GGATACAAGT
526494 ATGAAATGATGATGCAAAGCATG
1 ATGAAATGATGATGCAAAGCATG
*
526517 ATGAAATGATGATTCAAAGCATG
1 ATGAAATGATGATGCAAAGCATG
526540 TAACGTGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.09, G:0.24, T:0.24
Consensus pattern (23 bp):
ATGAAATGATGATGCAAAGCATG
Found at i:530391 original size:162 final size:165
Alignment explanation
Indices: 530022--530416 Score: 507
Period size: 162 Copynumber: 2.4 Consensus size: 165
530012 TAAAAAAATC
* * * **
530022 AAAAGGAATGAACTTTTCAAAAATAATTTTATGTGAATTGAATGATAATATTTGATGAATTTTAA
1 AAAATGAATGAATTTTTCAAAACTAA-TTTATGTGAATCAAATGATAATATTTGATGAATTTTAA
* ** * *
530087 AAATTTAAAATTGATGAAAATCCTCCCGAAAAGATTTGTGAAAAGGAAAACTTCGTATTTCGAAA
65 AAATTTAAAATCGATGAAAATCCTCCCGAAAAGAAATATGAAAAGGAAAACTTCGTATTTCAAAA
*
530152 ATATGTGGAATTCTAAGGAAAAATGAAAAACTCATG
130 ATATGAGGAATTCTAAGGAAAAATGAAAAACTCATG
* *
530188 AAAATGAATGAATTTTTCGAAACTGATTTAATGTGAATCAAATGATAATATTTGATGAATTTTAA
1 AAAATGAATGAATTTTTCAAAACTAATTT-ATGTGAATCAAATGATAATATTTGATGAATTTTAA
* *
530253 AAATTTTAAATCGATGAAAATCCTTCC-AAAA-AAATAT-AACGAA-GAAAAC-TCTGTATTTCA
65 AAATTTAAAATCGATGAAAATCCTCCCGAAAAGAAATATGAA--AAGGAAAACTTC-GTATTTCA
530313 AAAATATGAGG-ATT-TAAGGAAAAATGAAAAACTCATG
127 AAAATATGAGGAATTCTAAGGAAAAATGAAAAACTCATG
* * * * *
530350 AAAATGACTGAATTTTTTAAAACTAATTTAGTGTGAATCAAATTATAATATTTGATTAATTCTAA
1 AAAATGAATGAATTTTTCAAAACTAATTTA-TGTGAATCAAATGATAATATTTGATGAATTTTAA
530415 AA
65 AA
530417 TGTTAGGATC
Statistics
Matches: 202, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
161 1 0.00
162 81 0.40
163 7 0.03
164 26 0.13
165 9 0.04
166 78 0.39
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (165 bp):
AAAATGAATGAATTTTTCAAAACTAATTTATGTGAATCAAATGATAATATTTGATGAATTTTAAA
AATTTAAAATCGATGAAAATCCTCCCGAAAAGAAATATGAAAAGGAAAACTTCGTATTTCAAAAA
TATGAGGAATTCTAAGGAAAAATGAAAAACTCATG
Found at i:530780 original size:20 final size:20
Alignment explanation
Indices: 530734--530790 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
530724 TTGTATCGAT
*
530734 ACAATT-TATCGATACATGT
1 ACAATTGTATCGATACATGG
*
530753 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
530772 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
530791 AAACTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.09
19 14 0.42
20 16 0.48
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:530853 original size:13 final size:13
Alignment explanation
Indices: 530835--530865 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
530825 CGATACATGG
530835 TACATTGTATCGA
1 TACATTGTATCGA
530848 TACATTGTATCGA
1 TACATTGTATCGA
530861 TACAT
1 TACAT
530866 GATGAATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:530856 original size:33 final size:33
Alignment explanation
Indices: 530819--530886 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
530809 CTACCACTGT
*
530819 TTGTATCGATACATGGT-ACATTGTATCGATACA
1 TTGTATCGATACATGATGA-ATTGTATCGATACA
530852 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAATTGTATCGATACA
530885 TT
1 TT
530887 ACTTCTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATGAATTGTATCGATACA
Found at i:532162 original size:39 final size:40
Alignment explanation
Indices: 532090--532168 Score: 142
Period size: 39 Copynumber: 2.0 Consensus size: 40
532080 AATGGTTTAG
532090 GATACAATGCTTTTGAAAAAAGAAACAAAATTCAAGAATT
1 GATACAATGCTTTTGAAAAAAGAAACAAAATTCAAGAATT
*
532130 GATACAATGCTTTTG-AGAAAGAAACAAAATTCAAGAATT
1 GATACAATGCTTTTGAAAAAAGAAACAAAATTCAAGAATT
532169 TCTTTGTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 23 0.61
40 15 0.39
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (40 bp):
GATACAATGCTTTTGAAAAAAGAAACAAAATTCAAGAATT
Found at i:534024 original size:13 final size:13
Alignment explanation
Indices: 534006--534031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
533996 CATTTTGGGA
534006 TGTATCGATACAT
1 TGTATCGATACAT
534019 TGTATCGATACAT
1 TGTATCGATACAT
534032 CTTGTGTGTA
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:534737 original size:21 final size:21
Alignment explanation
Indices: 534711--534753 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
534701 TTTTCTTTTC
534711 TCTCCCCCTTAATAAAAAATT
1 TCTCCCCCTTAATAAAAAATT
* *
534732 TCTCCCCCTTAGTAAAATATT
1 TCTCCCCCTTAATAAAAAATT
534753 T
1 T
534754 TAACAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (21 bp):
TCTCCCCCTTAATAAAAAATT
Found at i:536176 original size:21 final size:21
Alignment explanation
Indices: 536132--536176 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
536122 GTGTGAGGGT
* *
536132 TGCCTGGTTGCGACCTGGGGG
1 TGCCTGGTCGCGACCTGGGAG
536153 TGCC-GGTCGCGACCTGGTGAG
1 TGCCTGGTCGCGACCTGG-GAG
536174 TGC
1 TGC
536177 TGCCTAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.07, C:0.27, G:0.44, T:0.22
Consensus pattern (21 bp):
TGCCTGGTCGCGACCTGGGAG
Found at i:536836 original size:8 final size:8
Alignment explanation
Indices: 536818--536848 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
536808 TTTTCAACAT
536818 CAAATATCA
1 CAAA-ATCA
536827 CAAAATCA
1 CAAAATCA
536835 CAAAATCA
1 CAAAATCA
536843 CAAAAT
1 CAAAAT
536849 TCAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.23, G:0.00, T:0.16
Consensus pattern (8 bp):
CAAAATCA
Found at i:542783 original size:13 final size:13
Alignment explanation
Indices: 542765--542803 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
542755 CATTTTGGGA
542765 TGTATCGATACAT
1 TGTATCGATACAT
*
542778 TGTATCAATACAT
1 TGTATCGATACAT
542791 TGTATCGATACAT
1 TGTATCGATACAT
542804 CTTGTGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:542910 original size:20 final size:21
Alignment explanation
Indices: 542863--542911 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
542853 GCCAATGACC
*
542863 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
542884 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
542904 TGTATCGA
1 TGTATCGA
542912 AATAATGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:546346 original size:13 final size:13
Alignment explanation
Indices: 546328--546352 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
546318 CATTTTATGG
546328 TGTATCGATACAA
1 TGTATCGATACAA
546341 TGTATCGATACA
1 TGTATCGATACA
546353 TACTGTGTGT
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:546368 original size:32 final size:33
Alignment explanation
Indices: 546305--546372 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
546295 CGTTACAAGC
**
546305 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
546338 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
546370 CAA
1 CAA
546373 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:548459 original size:21 final size:20
Alignment explanation
Indices: 548435--548477 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
548425 GGCTAGTGTA
*
548435 GGGGATGCCCGGTTACGACCT
1 GGGGATG-CCGGTCACGACCT
* *
548456 GGGGGTGCCGGTCGCGACCT
1 GGGGATGCCGGTCACGACCT
548476 GG
1 GG
548478 TGGGTGCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.47, T:0.16
Consensus pattern (20 bp):
GGGGATGCCGGTCACGACCT
Found at i:548936 original size:13 final size:13
Alignment explanation
Indices: 548918--548942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
548908 ATAATCCCCT
548918 TGTATCGATACAA
1 TGTATCGATACAA
548931 TGTATCGATACA
1 TGTATCGATACA
548943 CTAGAATATG
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:554351 original size:13 final size:13
Alignment explanation
Indices: 554333--554357 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
554323 CATTTTATGG
554333 TGTATCGATACAA
1 TGTATCGATACAA
554346 TGTATCGATACA
1 TGTATCGATACA
554358 TACTGTGTGT
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:554373 original size:32 final size:33
Alignment explanation
Indices: 554310--554377 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
554300 CATTACAAGC
**
554310 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
554343 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
554375 CAA
1 CAA
554378 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:554456 original size:20 final size:21
Alignment explanation
Indices: 554409--554461 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
554399 GCCAATGACT
**
554409 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
554430 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
554450 TGTATCGATACA
1 TGTATCGATACA
554462 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:554467 original size:13 final size:13
Alignment explanation
Indices: 554449--554473 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
554439 ACATTTGGTC
554449 ATGTATCGATACA
1 ATGTATCGATACA
554462 ATGTATCGATAC
1 ATGTATCGATAC
554474 TGTGCAACAT
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:555900 original size:13 final size:13
Alignment explanation
Indices: 555882--555906 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
555872 CAATATGCTT
555882 TGTATCGATACAA
1 TGTATCGATACAA
555895 TGTATCGATACA
1 TGTATCGATACA
555907 TGGGCAATTG
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:558453 original size:19 final size:19
Alignment explanation
Indices: 558428--558484 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
558418 TTATATCGAT
*
558428 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
558447 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
*
558466 ACAATTATATCGATACATG
1 AC-ATTGTATCGATACATG
558485 AAACTGGCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:564017 original size:20 final size:20
Alignment explanation
Indices: 563989--564042 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
563979 CTGCCAGTTT
* * **
563989 CATGCATCGATACAATTGTG
1 CATGTATCGATACAAGTGAA
564009 CATGTATCGATAC-AGTGAA
1 CATGTATCGATACAAGTGAA
564028 CATGTATCGATACAA
1 CATGTATCGATACAA
564043 AGCATACTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (20 bp):
CATGTATCGATACAAGTGAA
Found at i:565723 original size:25 final size:26
Alignment explanation
Indices: 565689--565739 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
565679 TCTTTGTTAA
565689 GTGTATTAGGT-AAACATATTAGGTG
1 GTGTATTAGGTGAAACATATTAGGTG
* *
565714 GTGTGTTAGGTGAAGCATATTAGGTG
1 GTGTATTAGGTGAAACATATTAGGTG
565740 TGTTAGGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.35
Consensus pattern (26 bp):
GTGTATTAGGTGAAACATATTAGGTG
Found at i:565742 original size:25 final size:24
Alignment explanation
Indices: 565689--565749 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 24
565679 TCTTTGTTAA
*
565689 GTGTATTAGGT-AAACATATTAGGTG
1 GTGTGTTAGGTGAAACATATTA-G-G
*
565714 GTGTGTTAGGTGAAGCATATTA-G
1 GTGTGTTAGGTGAAACATATTAGG
565737 GTGTGTTAGGTGA
1 GTGTGTTAGGTGA
565750 TGTATTTGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 14 0.42
25 10 0.30
26 9 0.27
ACGTcount: A:0.26, C:0.03, G:0.34, T:0.36
Consensus pattern (24 bp):
GTGTGTTAGGTGAAACATATTAGG
Found at i:565760 original size:21 final size:22
Alignment explanation
Indices: 565712--565760 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
565702 ACATATTAGG
565712 TGGTGTGTTAGGTGAAGCATATT
1 TGGTGTGTTAGGTGAAG-ATATT
* *
565735 AGGTGTGTTAGGTGATG-TATT
1 TGGTGTGTTAGGTGAAGATATT
565756 TGGTG
1 TGGTG
565761 AGAATATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 8 0.35
23 15 0.65
ACGTcount: A:0.18, C:0.02, G:0.39, T:0.41
Consensus pattern (22 bp):
TGGTGTGTTAGGTGAAGATATT
Found at i:565773 original size:34 final size:34
Alignment explanation
Indices: 565730--565898 Score: 293
Period size: 34 Copynumber: 5.0 Consensus size: 34
565720 TAGGTGAAGC
*
565730 ATATTAGGTGTGTTAGGTGATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
565764 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
565798 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* *
565832 ATATTAGATGTGTTAGGTAATGTATTTGGTGAAA
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
* *
565866 ATATTAGGTGTGTTAGGTAATGTGTTAGGTGAG
1 ATATTAGGTGTGTTAGGTAATGTATTTGGTGAG
565899 TAAGATATTT
Statistics
Matches: 128, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 128 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.41
Consensus pattern (34 bp):
ATATTAGGTGTGTTAGGTAATGTATTTGGTGAGA
Found at i:570681 original size:34 final size:34
Alignment explanation
Indices: 570638--570765 Score: 202
Period size: 34 Copynumber: 3.8 Consensus size: 34
570628 AGCATAGTCA
* *
570638 GTGTGTTAGGTGATGTCTTTGGTGAGAATATTAG
1 GTGTGTTAGGTAATGTATTTGGTGAGAATATTAG
570672 GTGTGTTAGGTAATGTATTTGGTGAGAATATTAG
1 GTGTGTTAGGTAATGTATTTGGTGAGAATATTAG
* *
570706 ATGTGTTAGGTAATGTATTTGGTGAAAATATTAG
1 GTGTGTTAGGTAATGTATTTGGTGAGAATATTAG
* *
570740 GTGTGTTAGGTAATGTGTTAGGTGAG
1 GTGTGTTAGGTAATGTATTTGGTGAG
570766 TAAGATATTT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 86 1.00
ACGTcount: A:0.25, C:0.01, G:0.34, T:0.41
Consensus pattern (34 bp):
GTGTGTTAGGTAATGTATTTGGTGAGAATATTAG
Found at i:571494 original size:20 final size:22
Alignment explanation
Indices: 571452--571496 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
571442 GCAGTGGGTG
571452 TGGGAGCTGCCCGATTACGACC
1 TGGGAGCTGCCCGATTACGACC
* *
571474 TGGGAG-TG-CCGATTGCTACC
1 TGGGAGCTGCCCGATTACGACC
571494 TGG
1 TGG
571497 AGGTGGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.16, C:0.27, G:0.36, T:0.22
Consensus pattern (22 bp):
TGGGAGCTGCCCGATTACGACC
Found at i:571815 original size:21 final size:22
Alignment explanation
Indices: 571776--571818 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
571766 ATGATTTTAC
* *
571776 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
571798 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
571819 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:578130 original size:20 final size:20
Alignment explanation
Indices: 578107--578153 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
578097 TTCATGTGTT
**
578107 GATACAATTGTGCATGTATC
1 GATACAATTGAACATGTATC
578127 GATACAA-TGAACATGTATC
1 GATACAATTGAACATGTATC
578146 GATACAAT
1 GATACAAT
578154 GCATCGATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (20 bp):
GATACAATTGAACATGTATC
Found at i:584498 original size:33 final size:33
Alignment explanation
Indices: 584456--584518 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
584446 CCACTGTTTG
*
584456 TATCGATACATG-TCACATTGTATCGATACAATT
1 TATCGATACATGATCA-ATTGTATCAATACAATT
*
584489 TATCGATACATGATGAATTGTATCAATACA
1 TATCGATACATGATCAATTGTATCAATACA
584519 TTGCTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (33 bp):
TATCGATACATGATCAATTGTATCAATACAATT
Found at i:585551 original size:44 final size:44
Alignment explanation
Indices: 585331--585613 Score: 173
Period size: 44 Copynumber: 6.5 Consensus size: 44
585321 ATGAGGATGA
* *
585331 AAAG-AGTTTGACCAGGGTTA-AACCATCACGTCAAA-TATAA-G
1 AAAGAAGTTTGACCAGGG-CAGAACCATCACGTCAAACAATAATG
* * * *
585372 TAAGCAGAA-TTTAACCAAGGCAGAACCATCACGTCAAACGATAGTG
1 -AA--AGAAGTTTGACCAGGGCAGAACCATCACGTCAAACAATAATG
** * * * *
585418 AAAAGGGGTTTGACTA-GGCAAAAGCATCACGTCAAACAATAGTG
1 -AAAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACAATAATG
* * * * * * ******
585462 AAAGAAGGTTGACCAAGGTAAAACTATCACGTTAATTGGGGATG
1 AAAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACAATAATG
* * *
585506 AAAGGAGTTTGACGAGGGCAGAACCATCACGTTAAACAATAATG
1 AAAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACAATAATG
* * * **
585550 AAAGAAGTTTGACCAGGGTAGAACCATCACATCAAATAAGGATG
1 AAAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACAATAATG
* *
585594 AAAAAAGTTTGACCAAGGCA
1 AAAGAAGTTTGACCAGGGCA
585614 AAATTGTCAC
Statistics
Matches: 181, Mismatches: 52, Indels: 14
0.73 0.21 0.06
Matches are distributed among these distances:
42 2 0.01
43 12 0.07
44 154 0.85
45 10 0.06
46 3 0.02
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (44 bp):
AAAGAAGTTTGACCAGGGCAGAACCATCACGTCAAACAATAATG
Found at i:585578 original size:132 final size:132
Alignment explanation
Indices: 585390--585628 Score: 293
Period size: 132 Copynumber: 1.8 Consensus size: 132
585380 ATTTAACCAA
* * ** * * *
585390 GGCAGAACCATCACGTCAAACGATAGTGAAAAGGGGTTTGACTAGGCAAAAGCATCACGTCAAAC
1 GGCAGAACCATCACGTCAAACAATAATGAAAAGAAGTTTGACCAGGCAAAACCATCACATCAAAC
* *
585455 AATAG-TGAAAGAAGGTTGACCAAGGTAAAACTATCACGTTAATTGGGGATGAAAGGAGTTTGAC
66 AA-AGATGAAAAAAGGTTGACCAAGGCAAAACTATCACGTTAATTGGGGATGAAAGGAGTTTGAC
585519 GAG
130 GAG
* * *
585522 GGCAGAACCATCACGTTAAACAATAATG-AAAGAAGTTTGACCAGGGTAGAACCATCACATCAAA
1 GGCAGAACCATCACGTCAAACAATAATGAAAAGAAGTTTGACCA-GGCAAAACCATCACATCAAA
* * * * *
585586 TAAGGATGAAAAAAGTTTGACCAAGGCAAAATTGTCACGTTAA
65 CAAAGATGAAAAAAGGTTGACCAAGGCAAAACTATCACGTTAA
585629 ATAAGAATGA
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
131 13 0.15
132 75 0.85
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (132 bp):
GGCAGAACCATCACGTCAAACAATAATGAAAAGAAGTTTGACCAGGCAAAACCATCACATCAAAC
AAAGATGAAAAAAGGTTGACCAAGGCAAAACTATCACGTTAATTGGGGATGAAAGGAGTTTGACG
AG
Found at i:585624 original size:88 final size:88
Alignment explanation
Indices: 585306--585698 Score: 269
Period size: 88 Copynumber: 4.4 Consensus size: 88
585296 GAGTAGGGCT
* * ** * *
585306 AAACCATCACATTAAATGAGGATGAAAAGAGTTTGACCAGGGTTAAACCATCACGTCAAA-TATA
1 AAACCATCACATTAAATGAGGATGAAAAAAGTTTGACCAAGGCAAAACCATCACGTTAAACAATA
* * *
585370 A-GTAAGCAGAA-TTTAACCAAGGCA
66 ATG-AA--AGAAGTTTGACCAGGGTA
* * * * * ** * * *
585394 GAACCATCACGTCAAACGA-TAGTGAAAAGGGGTTTGA-CTAGGCAAAAGCATCACGTCAAACAA
1 AAACCATCACATTAAATGAGGA-TGAAAA-AAGTTTGACCAAGGCAAAACCATCACGTTAAACAA
* * *
585457 TAGTGAAAGAAGGTTGACCAAGGTA
64 TAATGAAAGAAGTTTGACCAGGGTA
* * * * ** * * *
585482 AAACTATCACGTTAATTGGGGATGAAAGGAGTTTGACGAGGGCAGAACCATCACGTTAAACAATA
1 AAACCATCACATTAAATGAGGATGAAAAAAGTTTGACCAAGGCAAAACCATCACGTTAAACAATA
585547 ATGAAAGAAGTTTGACCAGGGTA
66 ATGAAAGAAGTTTGACCAGGGTA
* * * *** * *
585570 GAACCATCACATCAAATAAGGATGAAAAAAGTTTGACCAAGGCAAAATTGTCACGTTAAATAAGA
1 AAACCATCACATTAAATGAGGATGAAAAAAGTTTGACCAAGGCAAAACCATCACGTTAAACAATA
* *
585635 ATGAAA-AAGGTTTAACCTGGGTGA
66 ATGAAAGAA-GTTTGACCAGGGT-A
* *
585659 TAACCGAT-ACAGTTAAATGAGGATGAAAAAGGTTTGACCA
1 AAACC-ATCACA-TTAAATGAGGATGAAAAAAGTTTGACCA
585699 GAATGGTAAC
Statistics
Matches: 237, Mismatches: 57, Indels: 20
0.75 0.18 0.06
Matches are distributed among these distances:
87 14 0.06
88 174 0.73
89 21 0.09
90 28 0.12
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.20
Consensus pattern (88 bp):
AAACCATCACATTAAATGAGGATGAAAAAAGTTTGACCAAGGCAAAACCATCACGTTAAACAATA
ATGAAAGAAGTTTGACCAGGGTA
Found at i:585771 original size:93 final size:92
Alignment explanation
Indices: 585665--585884 Score: 282
Period size: 93 Copynumber: 2.4 Consensus size: 92
585655 GTGATAACCG
* * *
585665 ATACAGTTAAATGAGGATGAAAAAGGTTTGACCAGAATGGTAACTGATACAATAAAATAAGGGTG
1 ATACAG-TAAATGATGATGAAAAAGGTTTGACCAGAATGGTAACCGATACAAGAAAATAAGGGTG
*
585730 GAAAAAGTTTGACCAGGTCCTAA-TGCCA
65 GAAAAAGTTTGACCAAGTCCTAACT-CCA
** * * *
585758 ATACAGTCAAATGATGATGAAAGGGGTTTGACTAGAGTGGTAACCGATACAGGAAAATAAGGGTG
1 ATACAGT-AAATGATGATGAAAAAGGTTTGACCAGAATGGTAACCGATACAAGAAAATAAGGGTG
*
585823 GAAAGAGTTTGACCAAGTCCTAACTCCA
65 GAAAAAGTTTGACCAAGTCCTAACTCCA
*
585851 ATACAGGTAAACGATGATGAAATAA-GTTTGACCA
1 ATACA-GTAAATGATGATGAAA-AAGGTTTGACCA
585885 AATACAGCCA
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
92 1 0.01
93 105 0.96
94 3 0.03
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (92 bp):
ATACAGTAAATGATGATGAAAAAGGTTTGACCAGAATGGTAACCGATACAAGAAAATAAGGGTGG
AAAAAGTTTGACCAAGTCCTAACTCCA
Found at i:585834 original size:46 final size:45
Alignment explanation
Indices: 585627--585837 Score: 145
Period size: 46 Copynumber: 4.6 Consensus size: 45
585617 TTGTCACGTT
* * * * * *
585627 AAATAAGAATGAAAAAGGTTTAACCTGGGTGATAACCGATACAGTT
1 AAATAAGGATGAAAAA-GTTTGACCAGAGTGGTAACCGATACAGTA
* * * *
585673 AAATGAGGATGAAAAAGGTTTGACCAGAATGGTAACTGATACAATA
1 AAATAAGGATGAAAAA-GTTTGACCAGAGTGGTAACCGATACAGTA
* ** * *
585719 AAATAAGGGTGGAAAAAGTTTGACCAG-GTCCTAATGCCAATACAGTC
1 AAATAAGGAT-GAAAAAGTTTGACCAGAGTGGTAA--CCGATACAGTA
* * ** * *
585766 AAATGATGATGAAAGGGGTTTGACTAGAGTGGTAACCGATACAGGA
1 AAATAAGGATGAAA-AAGTTTGACCAGAGTGGTAACCGATACAGTA
* *
585812 AAATAAGGGTGGAAAGAGTTTGACCA
1 AAATAAGGAT-GAAAAAGTTTGACCA
585838 AGTCCTAACT
Statistics
Matches: 124, Mismatches: 35, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
45 4 0.03
46 82 0.66
47 33 0.27
48 5 0.04
ACGTcount: A:0.41, C:0.11, G:0.26, T:0.22
Consensus pattern (45 bp):
AAATAAGGATGAAAAAGTTTGACCAGAGTGGTAACCGATACAGTA
Found at i:585855 original size:47 final size:46
Alignment explanation
Indices: 585718--585857 Score: 122
Period size: 46 Copynumber: 3.0 Consensus size: 46
585708 CTGATACAAT
* * *
585718 AAAATAAGGGTGGAAAAAGTTTGACCAGGTCCTAATGCCAATACAGT
1 AAAATAAGGGTGGAAAGAGTTTGACCAAGTCCTAAT-CCAATACAGG
* * * * * * ** *
585765 CAAATGATGAT-GAAAGGGGTTTGACTAGAGTGGTAA-CCGATACAGG
1 AAAATAAGGGTGGAAA-GAGTTTGACCA-AGTCCTAATCCAATACAGG
585811 AAAATAAGGGTGGAAAGAGTTTGACCAAGTCCTAACTCCAATACAGG
1 AAAATAAGGGTGGAAAGAGTTTGACCAAGTCCTAA-TCCAATACAGG
585858 TAAACGATGA
Statistics
Matches: 67, Mismatches: 21, Indels: 10
0.68 0.21 0.10
Matches are distributed among these distances:
45 6 0.09
46 28 0.42
47 28 0.42
48 5 0.07
ACGTcount: A:0.39, C:0.14, G:0.26, T:0.21
Consensus pattern (46 bp):
AAAATAAGGGTGGAAAGAGTTTGACCAAGTCCTAATCCAATACAGG
Found at i:585898 original size:35 final size:34
Alignment explanation
Indices: 585859--586404 Score: 520
Period size: 35 Copynumber: 15.6 Consensus size: 34
585849 CAATACAGGT
* *
585859 AAACGATGATGAAATAAGTTTGACCAAATACAGCC
1 AAACGATGATGAAA-AAGTTTGACCAGATACAACC
* * *
585894 AAACGATTATGAAAAAAGTTTGACCAGATATAGCC
1 AAACGATGATG-AAAAAGTTTGACCAGATACAACC
* * *
585929 AAAAGATGATGAAAAAAGTTTGACCAGATATAACT
1 AAACGATGATG-AAAAAGTTTGACCAGATACAACC
* * *** *
585964 AAACGATGGTGAAAAAGTTTAACCAGATATGGCT
1 AAACGATGATGAAAAAGTTTGACCAGATACAACC
* *
585998 AAACAATGATGAAAAGAGTTTAACCAGATACAACC
1 AAACGATGATGAAAA-AGTTTGACCAGATACAACC
* *
586033 AAATGATGATGAAAAGAGTTTAACCAGATACAACC
1 AAACGATGATGAAAA-AGTTTGACCAGATACAACC
* * * * *
586068 AAATGATGATGAAATGAGTTTGGCTAGATGCAACC
1 AAACGATGATGAAA-AAGTTTGACCAGATACAACC
* * *
586103 AAACGATGATGAAAGGAGTTT-AGCCAGATGCAGCC
1 AAACGATGATGAAA-AAGTTTGA-CCAGATACAACC
* * * * * *
586138 AAACAATGAAGAAAGGAGTTTGGCCAGATGCAACT
1 AAACGATGATGAAA-AAGTTTGACCAGATACAACC
586173 AAACGATGATGAAAAGAGTTTGACCAGATACAACC
1 AAACGATGATGAAAA-AGTTTGACCAGATACAACC
* * *
586208 AAACGATGATTAAAAGAGTTTGACCAAATATAACC
1 AAACGATGATGAAAA-AGTTTGACCAGATACAACC
*
586243 AAACGATGATGAAAAAAGTTTGACCAGATACGACC
1 AAACGATGATG-AAAAAGTTTGACCAGATACAACC
*
586278 AAACGATGATGAAAAGTGTTTGACCTA-ATACAACC
1 AAACGATGATGAAAA-AGTTTGACC-AGATACAACC
* * *
586313 AAATGACGATGAAAAGAGTTTGACCAGATACAGCC
1 AAACGATGATGAAAA-AGTTTGACCAGATACAACC
* * * *
586348 AAATGATGATGAAAATAGTTTAACCAGATACAGCA
1 AAACGATGATGAAAA-AGTTTGACCAGATACAACC
*
586383 AAATGATGATGAAAAAAGTTTG
1 AAACGATGATG-AAAAAGTTTG
586405 TTTGGTAAGA
Statistics
Matches: 441, Mismatches: 59, Indels: 22
0.84 0.11 0.04
Matches are distributed among these distances:
34 38 0.09
35 391 0.89
36 12 0.03
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (34 bp):
AAACGATGATGAAAAAGTTTGACCAGATACAACC
Found at i:586140 original size:105 final size:105
Alignment explanation
Indices: 585859--586404 Score: 596
Period size: 105 Copynumber: 5.2 Consensus size: 105
585849 CAATACAGGT
* * * *
585859 AAACGATGATGAAATA-AGTTTGACCAAATACAGCCAAACGATTATGAAAAAAGTTTGACCAGAT
1 AAACGATGATGAAA-AGAGTTTGACCAGATACAACCAAACGATGATGAAAAGAGTTTGACCAGAT
* * * *
585923 ATAGCCAAAAGATGATGAAAAAAGTTTGACCAGATATAACT
65 ACAGCCAAACGATGATGAAAAAAGTTTGACCAGATACAACC
* * *** * * *
585964 AAACGATGGTGAAAA-AGTTTAACCAGATATGGCTAAACAATGATGAAAAGAGTTTAACCAGATA
1 AAACGATGATGAAAAGAGTTTGACCAGATACAACCAAACGATGATGAAAAGAGTTTGACCAGATA
* * * *
586028 CAACCAAATGATGATGAAAAGAGTTTAACCAGATACAACC
66 CAGCCAAACGATGATGAAAAAAGTTTGACCAGATACAACC
* * * * * *
586068 AAATGATGATGAAATGAGTTTGGCTAGATGCAACCAAACGATGATGAAAGGAGTTT-AGCCAGAT
1 AAACGATGATGAAAAGAGTTTGACCAGATACAACCAAACGATGATGAAAAGAGTTTGA-CCAGAT
* * * ** * * *
586132 GCAGCCAAACAATGAAGAAAGGAGTTTGGCCAGATGCAACT
65 ACAGCCAAACGATGATGAAAAAAGTTTGACCAGATACAACC
* *
586173 AAACGATGATGAAAAGAGTTTGACCAGATACAACCAAACGATGATTAAAAGAGTTTGACCAAATA
1 AAACGATGATGAAAAGAGTTTGACCAGATACAACCAAACGATGATGAAAAGAGTTTGACCAGATA
* * *
586238 TAACCAAACGATGATGAAAAAAGTTTGACCAGATACGACC
66 CAGCCAAACGATGATGAAAAAAGTTTGACCAGATACAACC
* * *
586278 AAACGATGATGAAAAGTGTTTGACCTA-ATACAACCAAATGACGATGAAAAGAGTTTGACCAGAT
1 AAACGATGATGAAAAGAGTTTGACC-AGATACAACCAAACGATGATGAAAAGAGTTTGACCAGAT
* * * * *
586342 ACAGCCAAATGATGATGAAAATAGTTTAACCAGATACAGCA
65 ACAGCCAAACGATGATGAAAAAAGTTTGACCAGATACAACC
* *
586383 AAATGATGATGAAAAAAGTTTG
1 AAACGATGATGAAAAGAGTTTG
586405 TTTGGTAAGA
Statistics
Matches: 362, Mismatches: 75, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
104 87 0.24
105 273 0.75
106 2 0.01
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (105 bp):
AAACGATGATGAAAAGAGTTTGACCAGATACAACCAAACGATGATGAAAAGAGTTTGACCAGATA
CAGCCAAACGATGATGAAAAAAGTTTGACCAGATACAACC
Found at i:587068 original size:92 final size:92
Alignment explanation
Indices: 586782--587105 Score: 358
Period size: 92 Copynumber: 3.6 Consensus size: 92
586772 TTTGTGGTCA
* * * * * *
586782 TGTGATGCATCAATAGCATCTAGTGGCT--AAAAAAGGGATATGATTAGCAATGAGTGATCAGGA
1 TGTGATGCATCAATACCATCTAGTGGTTGGATAAAAGGGATATGATTAGGAATTAGTGATCGGGA
**
586845 TACCCTTGCCCCAAAAAGATAAGGCTT
66 TACCCTTGCCCCAAGGAGATAAGGCTT
*
586872 TGTGATGCATCAATACCATCTAGTGGTTAGG-T-GAAGGGCATATGATTAGGAA-TA-TG-T-GG
1 TGTGATGCATCAATACCATCTAGTGGTT-GGATAAAAGGG-ATATGATTAGGAATTAGTGATCGG
* * * * *
586931 GCTACACGTTGCCCTAAGGAAATTAGGCTT
64 GATAC-CCTTGCCCCAAGGAGATAAGGCTT
* * *
586961 TGTGATGCACCAATACTATCTAGTGGTTGGATAAAGGGGATATGATTAGGAATTAGTGATCGGGA
1 TGTGATGCATCAATACCATCTAGTGGTTGGATAAAAGGGATATGATTAGGAATTAGTGATCGGGA
*
587026 TACCCTTGCCCGAAGGAGATAAGGCTT
66 TACCCTTGCCCCAAGGAGATAAGGCTT
* * ** *
587053 TGTGATGTATCAATACCATTTAGTGGTTGGATAAAAAAGATATGATTGGGAAT
1 TGTGATGCATCAATACCATCTAGTGGTTGGATAAAAGGGATATGATTAGGAAT
587106 ATGTGGTTTC
Statistics
Matches: 192, Mismatches: 31, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
88 7 0.04
89 59 0.31
90 34 0.18
91 8 0.04
92 78 0.41
93 6 0.03
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.28
Consensus pattern (92 bp):
TGTGATGCATCAATACCATCTAGTGGTTGGATAAAAGGGATATGATTAGGAATTAGTGATCGGGA
TACCCTTGCCCCAAGGAGATAAGGCTT
Found at i:587098 original size:181 final size:179
Alignment explanation
Indices: 586782--587111 Score: 450
Period size: 181 Copynumber: 1.8 Consensus size: 179
586772 TTTGTGGTCA
*
586782 TGTGATGCATCAATAGCATCTAGTGGCTAAAAAAGGGATATGATTAGCAATGAGTGATCAGGATA
1 TGTGATGCACCAATAGCATCTAGTGGCTAAAAAAGGGATATGATTAGCAATGAGTGATCAGGATA
* **
586847 CCCTTGCCCCAAAAAGATAAGGCTTTGTGATGCATCAATACCATCTAGTGGTTAGGTGAAGGGCA
66 CCCTTGCCCCAAAAAGATAAGGCTTTGTGATGCATCAATACCATCTAGTGGTTAGGTAAAAAGCA
586912 TATGATTAGGAATATGTGGGCTACACGTTGCCCTAAGGAAATTAGGCTT
131 TATGATTAGGAATATGTGGGCTACACGTTGCCCTAAGGAAATTAGGCTT
* * * * * *
586961 TGTGATGCACCAATA-CTATCTAGTGGTTGGATAAAGGGGATATGATTAGGAATTAGTGATCGGG
1 TGTGATGCACCAATAGC-ATCTAGTGGCT--AAAAAAGGGATATGATTAGCAATGAGTGATCAGG
* ** * *
587025 ATACCCTTGCCCGAAGGAGATAAGGCTTTGTGATGTATCAATACCATTTAGTGGTT-GGATAAAA
63 ATACCCTTGCCCCAAAAAGATAAGGCTTTGTGATGCATCAATACCATCTAGTGGTTAGG-T-AAA
*
587089 AAG-ATATGATTGGGAATATGTGG
126 AAGCATATGATTAGGAATATGTGG
587112 TTTCCACAAT
Statistics
Matches: 130, Mismatches: 16, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
178 1 0.01
179 24 0.18
180 2 0.02
181 100 0.77
182 3 0.02
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (179 bp):
TGTGATGCACCAATAGCATCTAGTGGCTAAAAAAGGGATATGATTAGCAATGAGTGATCAGGATA
CCCTTGCCCCAAAAAGATAAGGCTTTGTGATGCATCAATACCATCTAGTGGTTAGGTAAAAAGCA
TATGATTAGGAATATGTGGGCTACACGTTGCCCTAAGGAAATTAGGCTT
Found at i:587688 original size:89 final size:89
Alignment explanation
Indices: 587549--587718 Score: 236
Period size: 89 Copynumber: 1.9 Consensus size: 89
587539 TAAGATTATG
** * *
587549 CAAATACTAATGTCATCTAATGGTGCAGATATGTGTGAAATAATGCAAATGCAAGCATCAGTAAA
1 CAAATACTAATGTCATCTAATAATGCAGATATGTGTGAAACAATGCAAATGCAAGCATCAAT-AA
*
587614 AAAGGCAAATGTATATGGAATAATA
65 AAAGGCAAATGCATATGGAATAATA
* * *
587639 CAAATACTAATGTTATCTAA-AATGCAGATGTAG-GTGAAACGATGCAAATGCAAGCATCAATAA
1 CAAATACTAATGTCATCTAATAATGCAGATAT-GTGTGAAACAATGCAAATGCAAGCATCAATAA
587702 AAAGGCAAATGCATATG
65 AAAGGCAAATGCATATG
587719 AAATGGCATA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
88 18 0.25
89 33 0.46
90 20 0.28
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (89 bp):
CAAATACTAATGTCATCTAATAATGCAGATATGTGTGAAACAATGCAAATGCAAGCATCAATAAA
AAGGCAAATGCATATGGAATAATA
Found at i:587842 original size:17 final size:17
Alignment explanation
Indices: 587820--587861 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
587810 CTAAAAAATA
*
587820 TTTTTGTTTTCTTTTTT
1 TTTTTGTTTTCTATTTT
*
587837 TTTTTGTTTTGTATTTT
1 TTTTTGTTTTCTATTTT
*
587854 GTTTTGTT
1 TTTTTGTT
587862 AAAACTTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.83
Consensus pattern (17 bp):
TTTTTGTTTTCTATTTT
Found at i:590225 original size:42 final size:42
Alignment explanation
Indices: 590153--590245 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
590143 TATCGAAAGC
* * * *
590153 CCAATAAAATACATAAGTTTTTCTTTTTCTCTTTTATATCTCA
1 CCAA-AAAATAAATAAGTTTTTATTATTCTCTTTTATATCCCA
590196 CCAAAAAATAAATAAGTTTTTATTATTCTCTTTTATATCCCA
1 CCAAAAAATAAATAAGTTTTTATTATTCTCTTTTATATCCCA
*
590238 CCAGAAAA
1 CCAAAAAA
590246 CTAGAGGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 41 0.91
43 4 0.09
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (42 bp):
CCAAAAAATAAATAAGTTTTTATTATTCTCTTTTATATCCCA
Found at i:591356 original size:156 final size:155
Alignment explanation
Indices: 590965--592079 Score: 1031
Period size: 155 Copynumber: 7.1 Consensus size: 155
590955 ACCTTAGGAA
** ** * * *
590965 TATACCTTTAACATGAAAGTATCCTAGTAACCCTAAAAGACTTAAAAAGGATTATTGATGGTATG
1 TATACCTTCGACATGAAAGTATCCCGGTAACCCTAAAAGACTTAAAAAGG-TTATAGCTGGGATG
* * * * * * *
591030 AACCTAGCCTAAATACCCACCTTCAACATAAAAGCGA-GTCGATGATAACCTAGGACTTGATTCC
65 AACCTATCCTAAATACCCACCTTCAACATAAAAGCGACCT-GGTGACAACCTAGGACTCGGTTCT
* * * * *
591094 GGTAAATTTTGAAAATACCCTTAAAGG
129 AGAAAATTATGAAAATACCCCTATAGG
* * * * * ** * * *
591121 -ATACCTTCAACTTAAAAGCA-CCCGATGCCCCTAAAGGACTTGAAAAATGATTATAGATGGGAT
1 TATACCTTCGACATGAAAGTATCCCGGTAACCCTAAAAGACTT-AAAAA-GGTTATAGCTGGGAT
* *** * * * * * * *
591184 GAACCTATCCTAAATACCTACCTTTGGCATAAAAGTGGCTTGGTAATAACTTAAGACTCGGTTCT
64 GAACCTATCCTAAATACCCACCTTCAACATAAAAGCGACCTGGTGACAACCTAGGACTCGGTTCT
* *
591249 AGAAAATTATGAAAATGCCCCCTAAAGG
129 AGAAAATTATGAAAAT-ACCCCTATAGG
* **
591277 TATACCTTTGACATGAAAGTATCCCGGTAACCCTAAAAGACTTAAAAATATTATAGCTAGGG-TG
1 TATACCTTCGACATGAAAGTATCCCGGTAACCCTAAAAGACTTAAAAAGGTTATAGCT-GGGATG
* *** *** *
591341 AACCTATCCTAAATACCCACCTTCGATA-AAAAAATTAACCCAATGACAACCTAGGACTCAGTTC
65 AACCTATCCTAAATACCCACCTTC-A-ACATAAAAGCGACCTGGTGACAACCTAGGACTCGGTTC
* **
591405 TA-AAAATTACGAAAATACCTATATAGG
128 TAGAAAATTATGAAAATACCCCTATAGG
* * * *
591432 TATTCCTTCGACATGAAACTATCCCGGTAA-CCTCAAAGAACTTAAAAAGGTTATAGCTGGGGTG
1 TATACCTTCGACATGAAAGTATCCCGGTAACCCTAAAAG-ACTTAAAAAGGTTATAGCTGGGATG
* * * * ** * *
591496 AACCTGTCCTAAATACCCACTTTCAACATAAAAGCGAACCTAGTGGCAACCTAAAACTAGTTTCT
65 AACCTATCCTAAATACCCACCTTCAACATAAAAGCG-ACCTGGTGACAACCTAGGACTCGGTTCT
*
591561 AGAAAAAATTATGAAAATACCCCTATGGG
129 AG--AAAATTATGAAAATACCCCTATAGG
* * * ** *
591590 TATATCTTCGACATAAAAGTTTCCTAGTAACCCTAAAAGACATAAAAAGGTTATAGCTGGGATGA
1 TATACCTTCGACATGAAAGTATCCCGGTAACCCTAAAAGACTTAAAAAGGTTATAGCTGGGATGA
* * *** * *
591655 ACCTATCCTAAATACCCACCTTCAGCATAAAAGCAAACCAAATGACAACCTAGGACTCGATTTTA
66 ACCTATCCTAAATACCCACCTTCAACATAAAAGC-GACCTGGTGACAACCTAGGACTCGGTTCTA
* *
591720 AAAAATTATGAAAATACCCCTATGGG
130 GAAAATTATGAAAATACCCCTATAGG
* * * **
591746 TATATCTTCGACATAAAAGTTTCCTAGTAACCCTAAAAGACTTAAAAAGGTTATAGCTGGGATGA
1 TATACCTTCGACATGAAAGTATCCCGGTAACCCTAAAAGACTTAAAAAGGTTATAGCTGGGATGA
* * * *
591811 ACCTATCCTAAATACCCACCTTCGATAAAAAAGCAGACCTGGTGACAACCTAGGACTCAGTTCTA
66 ACCTATCCTAAATACCCACCTTCAACATAAAAGC-GACCTGGTGACAACCTAGGACTCGGTTCTA
* ** **
591876 GAAAACTACAAAAATGTCCCTATAGG
130 GAAAATTATGAAAATACCCCTATAGG
** * * *
591902 TATACCTTCGACATGAAAGT-TTTCGATAACCCTAAAAGACTAAAAAAGGTTATAGTTGGGATGA
1 TATACCTTCGACATGAAAGTATCCCGGTAACCCTAAAAGACTTAAAAAGGTTATAGCTGGGATGA
* * *
591966 ACCTATCATAAATACTCACCTTCAACATAAAAGCGGACCTGGTGACAACCTAAGACTCGGTTCTA
66 ACCTATCCTAAATACCCACCTTCAACATAAAAGC-GACCTGGTGACAACCTAGGACTCGGTTCTA
* * * *
592031 AAAAATTATGAAAATGCCCTTATAAG
130 GAAAATTATGAAAATACCCCTATAGG
* *
592057 CATACCTTCGACGTGAAAGTATC
1 TATACCTTCGACATGAAAGTATC
592080 TCGCAACCTA
Statistics
Matches: 781, Mismatches: 159, Indels: 38
0.80 0.16 0.04
Matches are distributed among these distances:
153 1 0.00
154 31 0.04
155 320 0.41
156 237 0.30
157 48 0.06
158 137 0.18
159 7 0.01
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (155 bp):
TATACCTTCGACATGAAAGTATCCCGGTAACCCTAAAAGACTTAAAAAGGTTATAGCTGGGATGA
ACCTATCCTAAATACCCACCTTCAACATAAAAGCGACCTGGTGACAACCTAGGACTCGGTTCTAG
AAAATTATGAAAATACCCCTATAGG
Found at i:594086 original size:20 final size:21
Alignment explanation
Indices: 594041--594092 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
594031 AACCCTGAAA
*
594041 AGTATCGATACACATTTAAAT
1 AGTATCGATACACAATTAAAT
**
594062 A-TATCGATACA-AATTGCAT
1 AGTATCGATACACAATTAAAT
594081 AGTATCGATACA
1 AGTATCGATACA
594093 TTGTATCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 6 0.22
20 20 0.74
21 1 0.04
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (21 bp):
AGTATCGATACACAATTAAAT
Found at i:594100 original size:13 final size:13
Alignment explanation
Indices: 594082--594106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
594072 AAATTGCATA
594082 GTATCGATACATT
1 GTATCGATACATT
594095 GTATCGATACAT
1 GTATCGATACAT
594107 GACCAAATGT
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):
GTATCGATACATT
Found at i:594119 original size:20 final size:21
Alignment explanation
Indices: 594094--594146 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
594084 ATCGATACAT
**
594094 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
594114 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
594135 TGTATCGATACA
1 TGTATCGATACA
594147 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:594204 original size:19 final size:20
Alignment explanation
Indices: 594180--594227 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
594170 TAGCCAAATT
*
594180 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
594199 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
594219 TGTATCGAT
1 TGTATCGAT
594228 GCATTGGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:599161 original size:13 final size:13
Alignment explanation
Indices: 599143--599178 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
599133 GCACCCTCTA
*
599143 TATCGATACATTG
1 TATCGATACAGTG
599156 TATCGATACAGTG
1 TATCGATACAGTG
599169 TATCGATACA
1 TATCGATACA
599179 AAGGGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:601059 original size:22 final size:22
Alignment explanation
Indices: 601033--601077 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
601023 CGAAAGTGTT
601033 AAATTATTTT-ACTAAGGGGGAG
1 AAATT-TTTTGACTAAGGGGGAG
*
601055 AAATTTTTTGATTAAGGGGGAG
1 AAATTTTTTGACTAAGGGGGAG
601077 A
1 A
601078 GAAAAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (22 bp):
AAATTTTTTGACTAAGGGGGAG
Found at i:601652 original size:13 final size:13
Alignment explanation
Indices: 601634--601658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
601624 AAATTGCATA
601634 GTATCGATACATT
1 GTATCGATACATT
601647 GTATCGATACAT
1 GTATCGATACAT
601659 GACCAAATGT
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):
GTATCGATACATT
Found at i:603197 original size:122 final size:122
Alignment explanation
Indices: 602955--603195 Score: 290
Period size: 122 Copynumber: 2.0 Consensus size: 122
602945 CTAAGGAAAA
* * * *
602955 ATGAAAATGAGTGAATTTTTCAAATATAATTTAATATGAATAGAATGATAATAATTAATGAATTT
1 ATGAAAATGAATGAATTTTTAAAATATAATCTAACATGAATAGAATGATAATAATTAATGAATTT
* * * * *
603020 TAAAAATTTTAAATTGATGAAAATCCTTCTAAAAAATTGAGGAAAGATGAAAAACTC
66 TAAAAATTTTAAATTGATAAAAATCCTTCAAAAAAATTGAGCAAAAAAGAAAAACTC
* * * *
603077 ATGAAAATGAATGAATATTTTAAAAT-TGATCTAACGTGAATCA-AATGATAATATTTGATGAAT
1 ATGAAAATGAATGAAT-TTTTAAAATATAATCTAACATGAAT-AGAATGATAATAATTAATGAAT
* *
603140 TTTAAAAATTTTATATTGATAAAAATCCTCTCGAAAAAAATTTA-CAAAAAAGAAAA
64 TTTAAAAATTTTAAATTGATAAAAATCCT-TC-AAAAAAATTGAGCAAAAAAGAAAA
603196 CTTTGTATTT
Statistics
Matches: 100, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
122 71 0.71
123 20 0.20
124 9 0.09
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (122 bp):
ATGAAAATGAATGAATTTTTAAAATATAATCTAACATGAATAGAATGATAATAATTAATGAATTT
TAAAAATTTTAAATTGATAAAAATCCTTCAAAAAAATTGAGCAAAAAAGAAAAACTC
Found at i:603790 original size:24 final size:22
Alignment explanation
Indices: 603750--603795 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
603740 CATGATAATA
603750 TTCACAGAAATAGTTTTTAAAAT
1 TTCACAGAAATAG-TTTTAAAAT
603773 TTCACAAGAAAGTA-TTTTAAAAT
1 TTCAC-AGAAA-TAGTTTTAAAAT
603796 AAAATTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 14 0.67
24 5 0.24
25 2 0.10
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (22 bp):
TTCACAGAAATAGTTTTAAAAT
Found at i:613418 original size:67 final size:67
Alignment explanation
Indices: 613339--613464 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 67
613329 GGTCTTTGTG
* * *
613339 AACTTGCATGTCAAAGGTGTACTTA-AGG-ATACGTTCATTATTTTTAGAGTCTTTTAAAGATGT
1 AACTTGCATGTCAAAGGCGTACTTAGAGGTATAC-TT-ATCATTTTTAAAGTCTTTTAAAGATGT
613402 CAAT
64 CAAT
* * *
613406 AACTTTCATGTCAAAGGCGTATTTAGGGGTATACTTATCATTTTTAAAGTCTTTTAAAG
1 AACTTGCATGTCAAAGGCGTACTTAGAGGTATACTTATCATTTTTAAAGTCTTTTAAAG
613465 TCACCGAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
67 43 0.84
68 4 0.08
69 4 0.08
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (67 bp):
AACTTGCATGTCAAAGGCGTACTTAGAGGTATACTTATCATTTTTAAAGTCTTTTAAAGATGTCA
AT
Found at i:616372 original size:33 final size:33
Alignment explanation
Indices: 616329--616392 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
616319 TGTAAAAATG
*
616329 TAGAGCTATTCTCAATAACATAAACAAATAATA
1 TAGAGATATTCTCAATAACATAAACAAATAATA
*
616362 TAGAGATATTCTTAATAACATAAACAAATAA
1 TAGAGATATTCTCAATAACATAAACAAATAA
616393 GAAAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (33 bp):
TAGAGATATTCTCAATAACATAAACAAATAATA
Found at i:616801 original size:21 final size:20
Alignment explanation
Indices: 616777--616824 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
616767 ATTAACCATA
616777 ATTGATAATTATCTTGTAGAT
1 ATTGATAATTATC-TGTAGAT
616798 ATTGGATAATTATCTGTAGAT
1 ATT-GATAATTATCTGTAGAT
616819 -TTGATA
1 ATTGATA
616825 CATTTAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.15
20 2 0.08
21 10 0.38
22 10 0.38
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTGATAATTATCTGTAGAT
Found at i:618005 original size:51 final size:51
Alignment explanation
Indices: 617926--618075 Score: 212
Period size: 51 Copynumber: 2.9 Consensus size: 51
617916 TTTAAAAATT
* **
617926 AAAATAGCTTTCGTACCTATCTATAAGACCAGAAA-AACACGAAAGCTTATC
1 AAAATATCTTTCGTACCTATCTGGAAGACCA-AAAGAACACGAAAGCTTATC
* * *
617977 AAAATATCTTTCATGCCTATCTGGAAGACTAAAAGAACACGAAAGCTTATC
1 AAAATATCTTTCGTACCTATCTGGAAGACCAAAAGAACACGAAAGCTTATC
* *
618028 AAAATATCTTTCGTACCTATTTGGAAGACCAAAAGAACAGGAAAGCTT
1 AAAATATCTTTCGTACCTATCTGGAAGACCAAAAGAACACGAAAGCTT
618076 CTTTATCATT
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 3 0.03
51 84 0.97
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (51 bp):
AAAATATCTTTCGTACCTATCTGGAAGACCAAAAGAACACGAAAGCTTATC
Found at i:619864 original size:21 final size:20
Alignment explanation
Indices: 619827--619865 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
619817 CACATTTTTA
619827 TCTAAATATATCAATACATT
1 TCTAAATATATCAATACATT
* *
619847 TCTAGAATGTATCGATACA
1 TCTA-AATATATCAATACA
619866 AGGTCCCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (20 bp):
TCTAAATATATCAATACATT
Found at i:621478 original size:12 final size:12
Alignment explanation
Indices: 621463--621489 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
621453 ATGTTTCCTG
621463 CTGGCAGCAACA
1 CTGGCAGCAACA
621475 CTGGCAGCAACA
1 CTGGCAGCAACA
621487 CTG
1 CTG
621490 TTTCCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.26, T:0.11
Consensus pattern (12 bp):
CTGGCAGCAACA
Found at i:633148 original size:1 final size:1
Alignment explanation
Indices: 633144--633217 Score: 67
Period size: 1 Copynumber: 74.0 Consensus size: 1
633134 CATTCTCCGC
* * * * * * * *
633144 AAAAAAAAAAACAAAAACAAAAACAAACAAAAAAAACAACAAAAAAACAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
633209 CAAAAAAAA
1 AAAAAAAAA
633218 CAAACAACGA
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:633175 original size:9 final size:9
Alignment explanation
Indices: 633143--633221 Score: 115
Period size: 9 Copynumber: 8.4 Consensus size: 9
633133 GCATTCTCCG
633143 CAAAAAAAA
1 CAAAAAAAA
633152 -AAACAAAAA
1 CAAA-AAAAA
633161 CAAAAACAAA
1 CAAAAA-AAA
633171 CAAAAAAAA
1 CAAAAAAAA
633180 CAACAAAAAAA
1 C-A-AAAAAAA
633191 CAAAAAAAA
1 CAAAAAAAA
633200 CAAAAAAAA
1 CAAAAAAAA
633209 CAAAAAAAA
1 CAAAAAAAA
633218 CAAA
1 CAAA
633222 CAACGAAAAG
Statistics
Matches: 65, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
8 3 0.05
9 40 0.62
10 14 0.22
11 8 0.12
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:633176 original size:29 final size:27
Alignment explanation
Indices: 633143--633221 Score: 113
Period size: 29 Copynumber: 2.8 Consensus size: 27
633133 GCATTCTCCG
*
633143 CAAAAAAAAAAACAAAAACAAAAACAAA
1 CAAAAAAAAAAAAAAAAACAAAAA-AAA
633171 CAAAAAAAACAACAAAAAAACAAAAAAAA
1 CAAAAAAAA-AA-AAAAAAACAAAAAAAA
*
633200 CAAAAAAAACAAAAAAAACAAA
1 CAAAAAAAAAAAAAAAAACAAA
633222 CAACGAAAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
27 11 0.23
28 10 0.21
29 14 0.30
30 12 0.26
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (27 bp):
CAAAAAAAAAAAAAAAAACAAAAAAAA
Found at i:633223 original size:42 final size:40
Alignment explanation
Indices: 633143--633230 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 40
633133 GCATTCTCCG
* *
633143 CAAAAAAAAAAACAAAAACAAAAACAAACAAAAAAAACAA
1 CAAAAAAAAAAAAAAAAAAAAAAACAAACAAAAAAAACAA
633183 CAAAAAAACAAAAAAAACAAAAAAAACAAA-AAAAACAAACAA
1 CAAAAAAA-AAAAAAAA-AAAAAAAACAAACAAAAA-AAACAA
*
633225 CGAAAA
1 CAAAAA
633231 GGGTTCGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 8 0.19
41 12 0.29
42 22 0.52
ACGTcount: A:0.84, C:0.15, G:0.01, T:0.00
Consensus pattern (40 bp):
CAAAAAAAAAAAAAAAAAAAAAAACAAACAAAAAAAACAA
Found at i:633224 original size:39 final size:40
Alignment explanation
Indices: 633143--633220 Score: 133
Period size: 38 Copynumber: 2.0 Consensus size: 40
633133 GCATTCTCCG
633143 CAAAAAAAAAAACAAAAACAAAAACAAACAAAAAAAACAA
1 CAAAAAAAAAAACAAAAACAAAAACAAACAAAAAAAACAA
*
633183 CAAAAAAACAAA-AAAAACAAAAA-AAACAAAAAAAACAA
1 CAAAAAAAAAAACAAAAACAAAAACAAACAAAAAAAACAA
633221 ACAACGAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
38 15 0.41
39 11 0.30
40 11 0.30
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (40 bp):
CAAAAAAAAAAACAAAAACAAAAACAAACAAAAAAAACAA
Found at i:634827 original size:27 final size:27
Alignment explanation
Indices: 634669--634937 Score: 270
Period size: 28 Copynumber: 9.7 Consensus size: 27
634659 CCTCACTTTC
* *
634669 CAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCAAC-CTT
634697 CAAAAGCCCACAAGTCAGTGGCAACCTT
1 C-AAAGCCCACAAGTCAGTGGCAACCTT
* * *
634725 CAGAAACCCACAAATCGGTGGCAACCTT
1 CA-AAGCCCACAAGTCAGTGGCAACCTT
634753 CAAAAGCCCACAAGTCAGTGGC-ACCTTTT
1 C-AAAGCCCACAAGTCAGTGGCAACC--TT
* * *
634782 CAAAGTCCATAAGTTAGTGGCAACCTT
1 CAAAGCCCACAAGTCAGTGGCAACCTT
** *
634809 CAAAGTACACAAATCAGTGGCAACCTT
1 CAAAGCCCACAAGTCAGTGGCAACCTT
* * * *
634836 CAAAAGTCCATAAGTTAGTGGCAAACTT
1 C-AAAGCCCACAAGTCAGTGGCAACCTT
* *
634864 CAAAGTCCATAAGTCAGTGGCAACCTT
1 CAAAGCCCACAAGTCAGTGGCAACCTT
* *
634891 CAAAACCCACAAGGCAGTGGCAACCTT
1 CAAAGCCCACAAGTCAGTGGCAACCTT
* *
634918 CAAAAGCACACAATTCAGTG
1 C-AAAGCCCACAAGTCAGTG
634938 TAACCCTTTC
Statistics
Matches: 203, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
27 78 0.38
28 96 0.47
29 29 0.14
ACGTcount: A:0.36, C:0.28, G:0.17, T:0.19
Consensus pattern (27 bp):
CAAAGCCCACAAGTCAGTGGCAACCTT
Found at i:634828 original size:55 final size:55
Alignment explanation
Indices: 634695--634937 Score: 251
Period size: 55 Copynumber: 4.4 Consensus size: 55
634685 GTGGCATCTT
* ** * * **
634695 TTCAAAAGCCCACAAGTCAGTGGCAACCTTCAGAAACCCACAAATCGGTGGCAACC
1 TTCAAAAGCACACAAGTCAGTGGCAACCTTCA-AAGTCCATAAGTTAGTGGCAACC
*
634751 TTCAAAAGCCCACAAGTCAGTGGC-ACCTTTTCAAAGTCCATAAGTTAGTGGCAACC
1 TTCAAAAGCACACAAGTCAGTGGCAACC--TTCAAAGTCCATAAGTTAGTGGCAACC
* * *
634807 TTC-AAAGTACACAAATCAGTGGCAACCTTCAAAAGTCCATAAGTTAGTGGCAAAC
1 TTCAAAAGCACACAAGTCAGTGGCAACCTTC-AAAGTCCATAAGTTAGTGGCAACC
* ** * **
634862 TTC-AAAGTC-CATAAGTCAGTGGCAACCTTCAAAACCCACAAGGCAGTGGCAACC
1 TTCAAAAG-CACACAAGTCAGTGGCAACCTTCAAAGTCCATAAGTTAGTGGCAACC
*
634916 TTCAAAAGCACACAATTCAGTG
1 TTCAAAAGCACACAAGTCAGTG
634938 TAACCCTTTC
Statistics
Matches: 159, Mismatches: 21, Indels: 15
0.82 0.11 0.08
Matches are distributed among these distances:
54 25 0.16
55 83 0.52
56 47 0.30
57 4 0.03
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.19
Consensus pattern (55 bp):
TTCAAAAGCACACAAGTCAGTGGCAACCTTCAAAGTCCATAAGTTAGTGGCAACC
Found at i:635196 original size:101 final size:100
Alignment explanation
Indices: 635020--635943 Score: 968
Period size: 101 Copynumber: 9.4 Consensus size: 100
635010 ATATTGGCAC
* * * *
635020 CTTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATTGGCATCTTCACCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATC
*
635085 GCTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
66 GCTGGCCTTGAATCAGCACATTGGCACCTTT-TCAT
* * * * *
635121 TTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAATGTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATC
* *
635186 GTTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
66 GCTGGCCTTGAATCAGCACATTGGCACCTTT-TCAT
* * *
635222 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG------CACCTTTAAGTCCAATGTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATC
* *
635281 GCTGGCCTTAAATCAGCACATTGGCACC--TTCAC
66 GCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* * *
635314 CTTTAAGTCCAACATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCACCTTTAAGTCCAAT
* * * *
635379 GTCGATGGCCTTGAATCAGCACATTAGCACC--TTCAC
63 ATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* * ** * *
635415 CTTTAAGTTCAATGTTACTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCACCTTTAAGTCCAAT
* *
635480 ATCGCTGGCCTTGAATTAGCATATTGGCA------C--
63 ATCGCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* * * *
635510 CTTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATTAGCACCTTCACCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATC
* *
635575 ACTGGCCTTGAATCAGCATATTGGCACCTTTGTCAT
66 GCTGGCCTTGAATCAGCACATTGGCACCTTT-TCAT
* * * *
635611 CTTTAAATCCAATATCGCTGGCCTTGAATCAGCATATTGG------CACCTTTAAGTCCAATGTT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATC
* *
635670 GCTGGCCTTAAATCAGCACATTGGCACC--TTCAC
66 GCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* * * * *
635703 CTTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATC
* * **
635768 GTTGGCCTTAAATCAGCACATTGGCACCTTAACCAT
66 GCTGGCCTTGAATCAGCACATTGGCACCTT-TTCAT
* * * * *
635804 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACATTCATCTTTAAGTTCGATATT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATC
* * *
635869 GTTGGCCTTGAATCAGTACATTGG--CTTTTTCAT
66 GCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
** * * *
635902 CTTTAAGTCTGATATCGTTGGCCTTGAATTAGCATATTGGCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA
635944 TCTTTAACAT
Statistics
Matches: 715, Mismatches: 81, Indels: 57
0.84 0.09 0.07
Matches are distributed among these distances:
92 123 0.17
93 3 0.00
95 125 0.17
97 1 0.00
98 83 0.12
99 4 0.01
101 376 0.53
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (100 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATC
GCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
Found at i:635272 original size:144 final size:141
Alignment explanation
Indices: 635122--635995 Score: 809
Period size: 144 Copynumber: 6.0 Consensus size: 141
635112 CTTTGTCATT
* * * * *
635122 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCACCTTTAAGTCCAATGTTG
1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
* *
635187 TTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATC
66 CTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATC
*
635252 AGCATATTGGCACC
128 AGCACATTGGCACC
* * *
635266 TTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATTGGCACCTTCACCTTTAAGTCCAACATCG
1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
*
635331 CTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGATGGCCTTGAATC
66 CTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATC
*
635396 AGCACATTAGCACCTTCACC
128 AGCACATT-G-----GCACC
* * *
635416 TTTAAGTTCAATGTTACTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATA
1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATA
* * *
635481 TCGCTGGCCTTGAATTAGCATATTGGCA----C--CTTTAAGTCCAATGTTGCTGGCCTTAAATC
63 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATC
*
635540 AGCACATTAGCACCTTCACC
128 AGCACATT-G-----GCACC
* ** * *
635560 TTTAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAATCCAATA
1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATA
* *
635625 TCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATGTTGCTGGCCTTAAATC
63 TCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATC
635684 AGCACATTGGCACCTTCACC
128 AGCACATTGG------CACC
* *
635704 TTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATATCG
1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
* * * *
635769 TTGGCCTTAAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATATCGCTGGCCTTGAATC
66 CTGGCCTTGAATCAGCATATTGGCACCTT---CATCTTTAAGTCCAATGTCGCTGGCCTTGAATC
635834 AGCACATTGGCACATTCATC
128 AGCACATTGG--CA--C--C
* * * * * *** **
635854 TTTAAGTTCGATATTGTTGGCCTTGAATCAGTACATTGGCTTTTTCATCTTTAAGTCTGATATCG
1 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
* * * * * * * * **
635919 TTGGCCTTGAATTAGCATATTGGCATCTTTAACATTCCTATGCCCAATGTTGCTGGCCTTGTCTC
66 CTGGCCTTGAATCAGCATATTGGCACCTTCATC-TT--TAAGTCCAATGTCGCTGGCCTTGAATC
635984 AGCACATTGGCA
128 AGCACATTGGCA
635996 TTCTTCTTCA
Statistics
Matches: 635, Mismatches: 64, Indels: 58
0.84 0.08 0.08
Matches are distributed among these distances:
141 42 0.07
142 1 0.00
143 1 0.00
144 343 0.54
145 1 0.00
146 3 0.00
147 2 0.00
148 6 0.01
150 192 0.30
152 1 0.00
153 43 0.07
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (141 bp):
TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCG
CTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGC
ACATTGGCACC
Found at i:635417 original size:245 final size:245
Alignment explanation
Indices: 634975--635948 Score: 1351
Period size: 245 Copynumber: 4.0 Consensus size: 245
634965 GGTGGCATCC
* *
634975 TCTTCTAAGTCTAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTAAGTCCAATGTTGCTG
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTG
*
635040 GCCTTAAATCAGCACATTGGCATCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
65 GCCTTAAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
* *
635105 TTGGCACCTTTGTCATTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTAGCACCTTCAC
130 TTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCAC
*
635170 CTTTAAGTCCAATGTTGTTGGCCTTGAATCAGCATATTGGCACCTTTGTCA
195 CTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCA
635221 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTGG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTGG
*
635286 CCTTAAATCAGCACATTGGCACCTTCACCTTTAAGTCCAACATCGCTGGCCTTGAATCAGCATAT
66 CCTTAAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
* *
635351 TGGCACCTTTGTCATCTTTAAGTCCAATGTCGATGGCCTTGAATCAGCACATTAGCACCTTCACC
131 TGGCACCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCACC
* *
635416 TTTAAGTTCAATGTTACTGGCCTTGAATCAGCATATTGGCACCTTTGTCA
196 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCA
*
635466 TCTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTAAGTCCAATGTTGCTGG
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTGG
* *
635531 CCTTAAATCAGCACATTAGCACCTTCACCTTTAAGTCCAATATCACTGGCCTTGAATCAGCATAT
66 CCTTAAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
* * *
635596 TGGCACCTTTGTCATCTTTAAATCCAATATCGCTGGCCTTGAATCAGCATATT-G-----GCACC
131 TGGCACCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCACC
* *
635655 TTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATTGGCACC--T-TCA
196 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCA
* * * * * *
635702 CCTTTAAGTCCAATGTTGCTGGCCTTAAATCAGCACATTGGCACTTTCATCTTTAAGTCCAATAT
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATGT
* * *
635767 CGTTGGCCTTAAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATATCGCTGGCCTTGAA
60 TGCTGGCCTTAAATCAGCACATTGGCACCTT---CACCTTTAAGTCCAATATCGCTGGCCTTGAA
* * * * * * * *
635832 TCAGCACATTGGCA-C-AT-TCATCTTTAAGTTCGATATTGTTGGCCTTGAATCAGTACATTGGC
122 TCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGC
*** * ** * * * * *
635894 TTTTTCATCTTTAAGTCTGATATCGTTGGCCTTGAATTAGCATATTGGCATCTTT
187 ACCTTCACCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTT
635949 AACATTCCTA
Statistics
Matches: 657, Mismatches: 54, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
236 40 0.06
237 1 0.00
239 43 0.07
240 1 0.00
242 77 0.12
243 2 0.00
244 2 0.00
245 449 0.68
246 4 0.01
248 37 0.06
250 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (245 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATGTTGCTGG
CCTTAAATCAGCACATTGGCACCTTCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATAT
TGGCACCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTCACC
TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCA
Found at i:636886 original size:13 final size:13
Alignment explanation
Indices: 636868--636894 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
636858 CATTATTCAA
636868 TGTATCGATACAT
1 TGTATCGATACAT
636881 TGTATCGATACAT
1 TGTATCGATACAT
636894 T
1 T
636895 AATCTTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:636891 original size:33 final size:33
Alignment explanation
Indices: 636848--636913 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
636838 GCCAAGGAAA
* *
636848 TGTATTGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTAATCAATGTATCGATACAT
**
636881 TGTATCGATACATTAATCTTTGTATCGATACAT
1 TGTATCGATACATTAATCAATGTATCGATACAT
636914 CTGGAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTAATCAATGTATCGATACAT
Found at i:640177 original size:20 final size:20
Alignment explanation
Indices: 640148--640200 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
640138 TACCACTGTT
* *
640148 TGTATTGATACATGGTAAAA
1 TGTATCGATACATGATAAAA
* * *
640168 TGTATCGATATATGATGAAT
1 TGTATCGATACATGATAAAA
640188 TGTATCGATACAT
1 TGTATCGATACAT
640201 TGCCTGTAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGATAAAA
Found at i:646390 original size:13 final size:13
Alignment explanation
Indices: 646372--646396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
646362 ACAATATTCC
646372 TTGTATCGATACA
1 TTGTATCGATACA
646385 TTGTATCGATAC
1 TTGTATCGATAC
646397 CTTATCCCCA
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:646661 original size:14 final size:14
Alignment explanation
Indices: 646642--646671 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
646632 CTTTGTTCAA
646642 ATCCATTTCCAAAC
1 ATCCATTTCCAAAC
646656 ATCCATTTCCAAAC
1 ATCCATTTCCAAAC
646670 AT
1 AT
646672 TCCTAGATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.33, G:0.00, T:0.30
Consensus pattern (14 bp):
ATCCATTTCCAAAC
Found at i:648234 original size:22 final size:22
Alignment explanation
Indices: 648209--648250 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
648199 TTTTTAAAGA
648209 TTTGACAAAAGGGGAGAAATGC
1 TTTGACAAAAGGGGAGAAATGC
* *
648231 TTTGATAAAGGGGGAGAAAT
1 TTTGACAAAAGGGGAGAAAT
648251 ATGTTTATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.21
Consensus pattern (22 bp):
TTTGACAAAAGGGGAGAAATGC
Found at i:648779 original size:13 final size:13
Alignment explanation
Indices: 648761--648787 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
648751 ACATTATGCT
648761 TTGTATCGATACA
1 TTGTATCGATACA
648774 TTGTATCGATACA
1 TTGTATCGATACA
648787 T
1 T
648788 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:648817 original size:20 final size:19
Alignment explanation
Indices: 648771--648827 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
648761 TTGTATCGAT
*
648771 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
648790 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
648809 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
648828 AAATTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:651566 original size:21 final size:21
Alignment explanation
Indices: 651533--651577 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
651523 TTGCAAGTTG
*
651533 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
651555 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
651575 AAA
1 AAA
651578 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:653401 original size:15 final size:15
Alignment explanation
Indices: 653381--653419 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
653371 TAAAAATGTC
*
653381 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
653396 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
*
653411 CCAAATGAA
1 CAAAATGAA
653420 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:655508 original size:13 final size:13
Alignment explanation
Indices: 655490--655528 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
655480 ACATTTTTCT
*
655490 TTGTATCAATACA
1 TTGTATCGATACA
655503 TTGTATCGATACA
1 TTGTATCGATACA
655516 TTGTATCGATACA
1 TTGTATCGATACA
655529 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:655673 original size:21 final size:21
Alignment explanation
Indices: 655649--655695 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
655639 AAATCTTTTG
655649 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
655670 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
655690 CAAAAT
1 CAAAAT
655696 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:655692 original size:20 final size:19
Alignment explanation
Indices: 655651--655693 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
655641 ATCTTTTGCA
655651 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
655671 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
655691 AAA
1 AAA
655694 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:659836 original size:28 final size:28
Alignment explanation
Indices: 659804--659862 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
659794 ATACAAAAGT
659804 TTTAATATTTGCATGTAAGCCCATAAAC
1 TTTAATATTTGCATGTAAGCCCATAAAC
659832 TTTAATATTTGCATGTAAGCCCATAAAC
1 TTTAATATTTGCATGTAAGCCCATAAAC
659860 TTT
1 TTT
659863 CTAAATTTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (28 bp):
TTTAATATTTGCATGTAAGCCCATAAAC
Found at i:660090 original size:22 final size:23
Alignment explanation
Indices: 660060--660103 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
660050 TATATAATTA
660060 AAATACAAAATTAAGCAT-CAAAG
1 AAATACAAAATT-AGCATACAAAG
*
660083 AAAT-CAAAGTTAGCATACAAA
1 AAATACAAAATTAGCATACAAA
660104 CACGTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.59, C:0.14, G:0.09, T:0.18
Consensus pattern (23 bp):
AAATACAAAATTAGCATACAAAG
Found at i:661746 original size:22 final size:19
Alignment explanation
Indices: 661718--661759 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
661708 CTGATTTAAT
661718 ATGAATTTAATAAAAATATTTA
1 ATGAATTT--TAAAAAT-TTTA
661740 ATGAATTTTAAAAATTTTA
1 ATGAATTTTAAAAATTTTA
661759 A
1 A
661760 ACTAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
ATGAATTTTAAAAATTTTA
Done.