Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 88 of 186
Found at i:28548587 original size:25 final size:25
Alignment explanation
Indices: 28548559--28548610 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
28548549 ATAATATTAC
28548559 TTAAGTACTTAAGCAAATCTATTGT
1 TTAAGTACTTAAGCAAATCTATTGT
28548584 TTAAGTACTTAAGCAAATCTATTGT
1 TTAAGTACTTAAGCAAATCTATTGT
28548609 TT
1 TT
28548611 TACTTAAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (25 bp):
TTAAGTACTTAAGCAAATCTATTGT
Found at i:28549156 original size:47 final size:47
Alignment explanation
Indices: 28549076--28549391 Score: 470
Period size: 47 Copynumber: 6.6 Consensus size: 47
28549066 GTATCTTTGA
*
28549076 ATGAATGTGAAAGTATATATATATGTGATAAGGCCTAATGGCCGACGTG
1 ATGAATGTGAAAG--TGTATATATGTGATAAGGCCTAATGGCCGACGTG
*
28549125 ATGAATGTGAGAGTGTATATATGTGATAAGGCCTAATGGCCGACGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTG
*
28549172 ATGAATGTGAGAGTGTATATATGTGATAAGGCCTAATGGCCGACGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTG
* *
28549219 ATGAATGTGAGAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTG
* *
28549266 ATGAATGTGAAAGTGTATATATATGTGATAGGGCCTAATGGCCGATGTG
1 ATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGACGTG
* * * * *
28549315 ATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTG
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTG
* *
28549362 ATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGAATGTGAAAGTGTATATATGTGATAAG
28549392 TCCCGAAGGG
Statistics
Matches: 251, Mismatches: 14, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
47 193 0.77
49 58 0.23
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTG
Found at i:28549334 original size:143 final size:141
Alignment explanation
Indices: 28549076--28549391 Score: 470
Period size: 143 Copynumber: 2.2 Consensus size: 141
28549066 GTATCTTTGA
* *
28549076 ATGAATGTGAAAGTATATATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGT
1 ATGAATGTGAAAG--TGTATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGT
* * *
28549141 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTATATATGTGATAAGGCCT
64 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCG
*
28549206 AATGGCCGACGTG
129 AATGGCCAACGTG
* *
28549219 ATGAATGTGAGAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG--T
* * *
28549284 ATATATGTGATAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCG
64 ATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCG
*
28549349 AGTGGCCAACGTG
129 AATGGCCAACGTG
* *
28549362 ATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGAATGTGAAAGTGTATATATGTGATAAG
28549392 TCCCGAAGGG
Statistics
Matches: 156, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
141 46 0.29
143 110 0.71
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (141 bp):
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTAT
ATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAA
TGGCCAACGTG
Found at i:28555118 original size:14 final size:14
Alignment explanation
Indices: 28555096--28555125 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28555086 TAATTATTAA
28555096 TAATGAAATAAAGT
1 TAATGAAATAAAGT
*
28555110 TAATTAAATAAAGT
1 TAATGAAATAAAGT
28555124 TA
1 TA
28555126 CACAAGCACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (14 bp):
TAATGAAATAAAGT
Found at i:28556819 original size:18 final size:15
Alignment explanation
Indices: 28556775--28556828 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 15
28556765 AAACCCTAGC
28556775 CCCAAAACCCAACAA
1 CCCAAAACCCAACAA
28556790 CCCACTAAACCCAACAGAA
1 CCCA--AAACCCAAC--AA
28556809 GCCCAAAACCCAACTAA
1 -CCCAAAACCCAAC-AA
28556826 CCC
1 CCC
28556829 TTAACCCCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 11 0.33
18 9 0.27
19 2 0.06
20 4 0.12
ACGTcount: A:0.46, C:0.46, G:0.04, T:0.04
Consensus pattern (15 bp):
CCCAAAACCCAACAA
Found at i:28558699 original size:12 final size:12
Alignment explanation
Indices: 28558686--28558759 Score: 64
Period size: 12 Copynumber: 6.3 Consensus size: 12
28558676 ATATTCTTAC
*
28558686 TATTATCATTAC
1 TATTATCATTAT
28558698 TA-TAT--TTAT
1 TATTATCATTAT
* *
28558707 TATCATCATCAT
1 TATTATCATTAT
*
28558719 TATTATTATTAT
1 TATTATCATTAT
*
28558731 TATTATTATTAT
1 TATTATCATTAT
*
28558743 TATTATCTTTACT
1 TATTATCATTA-T
28558756 TATT
1 TATT
28558760 TTCTCATTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
9 5 0.10
10 2 0.04
11 3 0.06
12 35 0.70
13 5 0.10
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATCATTAT
Found at i:28558723 original size:3 final size:3
Alignment explanation
Indices: 28558672--28558748 Score: 68
Period size: 3 Copynumber: 26.0 Consensus size: 3
28558662 TAATACTATA
* * * * * *
28558672 TAT TA- TAT TCT TAC TAT TAT CAT TAC TA- TATT TAT TAT CAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
28558716 CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28558749 CTTTACTTAT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
2 4 0.06
3 56 0.90
4 2 0.03
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:28564155 original size:21 final size:21
Alignment explanation
Indices: 28564108--28564167 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
28564098 ATAAAGAAGT
28564108 ATAAAAATTC--AAAAATAAA
1 ATAAAAATTCAAAAAAATAAA
28564127 ATGGAAAAATTCAAAAAAATAAA
1 AT--AAAAATTCAAAAAAATAAA
28564150 ATAAAACATT-AAAAAAAT
1 ATAAAA-ATTCAAAAAAAT
28564168 GCAACACGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 2 0.06
21 20 0.56
22 3 0.08
23 11 0.31
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.20
Consensus pattern (21 bp):
ATAAAAATTCAAAAAAATAAA
Found at i:28566067 original size:11 final size:12
Alignment explanation
Indices: 28566047--28566135 Score: 54
Period size: 12 Copynumber: 7.0 Consensus size: 12
28566037 TTCGTTTTGT
*
28566047 ATTATTTTTTAAA
1 ATTATTTTAT-AA
*
28566060 ATTATTTTATAT
1 ATTATTTTATAA
*
28566072 ATTATTTACTTTAA
1 ATTATTT--TATAA
*
28566086 ATTGTTTTATAA
1 ATTATTTTATAA
*
28566098 ATTATTTATTTCAA
1 ATTATTT-TAT-AA
*
28566112 ATTGA-TTTATAC
1 ATT-ATTTTATAA
*
28566124 TTTATTTTATAA
1 ATTATTTTATAA
28566136 TGTATATATT
Statistics
Matches: 58, Mismatches: 12, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
11 1 0.02
12 27 0.47
13 13 0.22
14 16 0.28
15 1 0.02
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (12 bp):
ATTATTTTATAA
Found at i:28566093 original size:26 final size:25
Alignment explanation
Indices: 28565962--28566130 Score: 116
Period size: 26 Copynumber: 6.6 Consensus size: 25
28565952 ATTTTGAACA
*
28565962 GTTTTAT-TATTATTTATTTTAAGTT
1 GTTTTATATATTATTTA-TTTAAATT
* ** *
28565987 -TTTTCCTATGGTATTTGTTCTAAATT
1 GTTTT-ATATATTATTTATT-TAAATT
* *
28566013 GTTTTACCATATTATTTATTTTAATT
1 GTTTTA-TATATTATTTATTTAAATT
*
28566039 CG-TTT-TGTATTATTT-TTTAAAATT
1 -GTTTTATATATTATTTATTT-AAATT
*
28566063 ATTTTATATATTATTTACTTTAAATT
1 GTTTTATATATTATTTA-TTTAAATT
*
28566089 GTTTTATAAATTATTTATTTCAAATT
1 GTTTTATATATTATTTATTT-AAATT
*
28566115 GATTTATACT-TTATTT
1 GTTTTATA-TATTATTT
28566131 TATAATGTAT
Statistics
Matches: 111, Mismatches: 20, Indels: 25
0.71 0.13 0.16
Matches are distributed among these distances:
23 3 0.03
24 19 0.17
25 15 0.14
26 57 0.51
27 17 0.15
ACGTcount: A:0.27, C:0.05, G:0.06, T:0.62
Consensus pattern (25 bp):
GTTTTATATATTATTTATTTAAATT
Found at i:28568371 original size:19 final size:19
Alignment explanation
Indices: 28568349--28568394 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
28568339 CTTCCTTTCT
28568349 TTTGCATT-CATTCCATACA
1 TTTGCATTGCATTCCAT-CA
*
28568368 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATTCCATCA
28568387 TTTGCATT
1 TTTGCATT
28568395 AAACTTTCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (19 bp):
TTTGCATTGCATTCCATCA
Found at i:28580292 original size:27 final size:27
Alignment explanation
Indices: 28580175--28580516 Score: 630
Period size: 27 Copynumber: 12.5 Consensus size: 27
28580165 CTATTTTTTT
28580175 GCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAGTC-AACTC
28580203 GCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAGTC-AACTC
28580231 GCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAGTC-AACTC
28580259 GCACACTTAGTGCTACATAGTCAACTC
1 GCACACTTAGTGCTACATAGTCAACTC
28580286 GCACACTTAGTGCTACATAGTCAACTC
1 GCACACTTAGTGCTACATAGTCAACTC
*
28580313 GCACACTTAGTGCTACATAATCAAACTC
1 GCACACTTAGTGCTACATAGTC-AACTC
28580341 GCACACTTAGTGCTACATAGTCAACTC
1 GCACACTTAGTGCTACATAGTCAACTC
28580368 GCACACTTAGTGCTACATAGTCAACTC
1 GCACACTTAGTGCTACATAGTCAACTC
28580395 GCACACTTAGTGCTACATAGTCAACTC
1 GCACACTTAGTGCTACATAGTCAACTC
28580422 GCACACTTAGTGCTACATAGTCAACTC
1 GCACACTTAGTGCTACATAGTCAACTC
28580449 GCACACTTAGTGCTACATAGTCAACTC
1 GCACACTTAGTGCTACATAGTCAACTC
*
28580476 GCACACTTAGTGCTACATAGTCAATTC
1 GCACACTTAGTGCTACATAGTCAACTC
28580503 GCACACTTAGTGCT
1 GCACACTTAGTGCT
28580517 GCACAATTTA
Statistics
Matches: 310, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
27 206 0.66
28 104 0.34
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
GCACACTTAGTGCTACATAGTCAACTC
Found at i:28580337 original size:82 final size:81
Alignment explanation
Indices: 28580175--28580516 Score: 630
Period size: 82 Copynumber: 4.2 Consensus size: 81
28580165 CTATTTTTTT
28580175 GCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
1 GCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAGTC-AACTCGCACACTTA
28580240 GTGCTACATAGTCAAACTC
64 GTGCTACATAGTC-AACTC
28580259 GCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGT
1 GCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGT
*
28580324 GCTACATAATCAAACTC
66 GCTACATAGTC-AACTC
28580341 GCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGT
1 GCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGT
28580406 GCTACATAGTCAACTC
66 GCTACATAGTCAACTC
28580422 GCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGT
1 GCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGT
*
28580487 GCTACATAGTCAATTC
66 GCTACATAGTCAACTC
28580503 GCACACTTAGTGCT
1 GCACACTTAGTGCT
28580517 GCACAATTTA
Statistics
Matches: 255, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
81 99 0.39
82 107 0.42
83 27 0.11
84 22 0.09
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
GCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGT
GCTACATAGTCAACTC
Found at i:28583474 original size:21 final size:22
Alignment explanation
Indices: 28583439--28583479 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28583429 GTTTATTTTG
28583439 ATGTTTGATGATAGA-AAATGT
1 ATGTTTGATGATAGATAAATGT
* *
28583460 ATGTTTGTTGTTAGATAAAT
1 ATGTTTGATGATAGATAAAT
28583480 AAAATTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (22 bp):
ATGTTTGATGATAGATAAATGT
Found at i:28585481 original size:26 final size:26
Alignment explanation
Indices: 28585444--28585493 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
28585434 TCATGGGCCG
* *
28585444 GGCTACTTGGCCCGGCCCGAAGGCTC
1 GGCTACTCGGCCCAGCCCGAAGGCTC
28585470 GGCTACTCGGCCCAGCCCGAAGGC
1 GGCTACTCGGCCCAGCCCGAAGGC
28585494 CCGCCCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.14, C:0.40, G:0.34, T:0.12
Consensus pattern (26 bp):
GGCTACTCGGCCCAGCCCGAAGGCTC
Found at i:28585796 original size:30 final size:31
Alignment explanation
Indices: 28585762--28585822 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
28585752 ACTTATTTTC
28585762 TTGTTAA-TTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTTGTTATTATTTTAAAGGCAT
* *
28585792 TTGTTAATTTTTTTTTATTATTTTAGAGGCA
1 TTGTTAA-TTTTTGTTATTATTTTAAAGGCA
28585823 CTTACTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 7 0.26
32 20 0.74
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.59
Consensus pattern (31 bp):
TTGTTAATTTTTGTTATTATTTTAAAGGCAT
Found at i:28586671 original size:23 final size:23
Alignment explanation
Indices: 28586641--28586721 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
28586631 CTTTCTTAAA
28586641 AATTGTTAATGATAGGAAGATTG
1 AATTGTTAATGATAGGAAGATTG
* * * * *
28586664 AATTGTTAGAATTAATTCA-TAAAAATA
1 AATTGTT--AA-TGA-T-AGGAAGATTG
28586691 AATTGTTAATGATAGGAAGATTG
1 AATTGTTAATGATAGGAAGATTG
28586714 AATTGTTA
1 AATTGTTA
28586722 GAATTAATTC
Statistics
Matches: 42, Mismatches: 10, Indels: 12
0.66 0.16 0.19
Matches are distributed among these distances:
22 1 0.02
23 20 0.48
24 2 0.05
25 4 0.10
26 2 0.05
27 12 0.29
28 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.19, T:0.37
Consensus pattern (23 bp):
AATTGTTAATGATAGGAAGATTG
Found at i:28586696 original size:50 final size:50
Alignment explanation
Indices: 28586640--28586735 Score: 192
Period size: 50 Copynumber: 1.9 Consensus size: 50
28586630 CCTTTCTTAA
28586640 AAATTGTTAATGATAGGAAGATTGAATTGTTAGAATTAATTCATAAAAAT
1 AAATTGTTAATGATAGGAAGATTGAATTGTTAGAATTAATTCATAAAAAT
28586690 AAATTGTTAATGATAGGAAGATTGAATTGTTAGAATTAATTCATAA
1 AAATTGTTAATGATAGGAAGATTGAATTGTTAGAATTAATTCATAA
28586736 TGATTTAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.36
Consensus pattern (50 bp):
AAATTGTTAATGATAGGAAGATTGAATTGTTAGAATTAATTCATAAAAAT
Found at i:28586860 original size:41 final size:41
Alignment explanation
Indices: 28586813--28586898 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
28586803 GATTACTCTA
28586813 GATACACAAAGGTTTATCTCCTAAGATCAAAAGATGAAACT
1 GATACACAAAGGTTTATCTCCTAAGATCAAAAGATGAAACT
28586854 GATACACAAAGGTTTATCTCCTAAGATCAAAAGATGAAACT
1 GATACACAAAGGTTTATCTCCTAAGATCAAAAGATGAAACT
28586895 GATA
1 GATA
28586899 AAACTTTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.24
Consensus pattern (41 bp):
GATACACAAAGGTTTATCTCCTAAGATCAAAAGATGAAACT
Found at i:28588748 original size:68 final size:68
Alignment explanation
Indices: 28588639--28588932 Score: 347
Period size: 68 Copynumber: 4.3 Consensus size: 68
28588629 GAGAGAGGTT
* ** * * * * *
28588639 TAATATGTAAGACCATTGCTAAACTATGGCAACATAAAGAGTTCGCCAAGATAGTAAACATGGGT
1 TAATATGTAAGACCATAGCTAGGCTATGGCAACATATAGAGTCCTCCAGGACAGTAAACATGGGT
28588704 TTA
66 TTA
* * * *
28588707 TAATATGTAAAACCATAGCTAGGCTATGGAAACATATAGAGTCTTCCAGGACAGTAAACATAGGT
1 TAATATGTAAGACCATAGCTAGGCTATGGCAACATATAGAGTCCTCCAGGACAGTAAACATGGGT
28588772 TTA
66 TTA
* * * *
28588775 TAATGTGTGAGACCATAGCTAGGCTATAGCAACATATAGAGTCCAT-CAGGATAGTAAACATGGG
1 TAATATGTAAGACCATAGCTAGGCTATGGCAACATATAGAGTCC-TCCAGGACAGTAAACATGGG
28588839 TTTA
65 TTTA
* * * *
28588843 TAATGTGTAAGACCATAACTAGGCTATGGCAATATATAGAGTCCTCCAGGACATTAAACATGGGT
1 TAATATGTAAGACCATAGCTAGGCTATGGCAACATATAGAGTCCTCCAGGACAGTAAACATGGGT
*
28588908 TCA
66 TTA
* * * *
28588911 TACTGTGTAAGACTATGGCTAG
1 TAATATGTAAGACCATAGCTAG
28588933 ACTACGGCCA
Statistics
Matches: 193, Mismatches: 31, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
67 1 0.01
68 191 0.99
69 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (68 bp):
TAATATGTAAGACCATAGCTAGGCTATGGCAACATATAGAGTCCTCCAGGACAGTAAACATGGGT
TTA
Found at i:28591412 original size:45 final size:45
Alignment explanation
Indices: 28591361--28591528 Score: 246
Period size: 45 Copynumber: 3.7 Consensus size: 45
28591351 CAATGTCGAT
* * * *
28591361 GTCCCAGACATGCTCTTACACGTAACCACATATATCGATGCCAAC
1 GTCCCAGACGTGGTCTTACACGAAATCACATATATCGATGCCAAC
* * * *
28591406 GTCCCAGACGTGGTCTTACACGAAATCACATTTATTGATGCAAAT
1 GTCCCAGACGTGGTCTTACACGAAATCACATATATCGATGCCAAC
*
28591451 GTCCCAGACGTGGTCTTACATGAAATCACATATATCGATGCCAAC
1 GTCCCAGACGTGGTCTTACACGAAATCACATATATCGATGCCAAC
*
28591496 GTCCCAGACGTGGTCTTACACAAAATCACATAT
1 GTCCCAGACGTGGTCTTACACGAAATCACATAT
28591529 CAGAATCCTA
Statistics
Matches: 108, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 108 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (45 bp):
GTCCCAGACGTGGTCTTACACGAAATCACATATATCGATGCCAAC
Found at i:28591468 original size:90 final size:90
Alignment explanation
Indices: 28591359--28591526 Score: 282
Period size: 90 Copynumber: 1.9 Consensus size: 90
28591349 TACAATGTCG
*
28591359 ATGTCCCAGACATGCTCTTACACGTAACCACATATATCGATGCCAACGTCCCAGACGTGGTCTTA
1 ATGTCCCAGACATGCTCTTACACGAAACCACATATATCGATGCCAACGTCCCAGACGTGGTCTTA
*
28591424 CACGAAATCACATTTATTGATGCAA
66 CACAAAATCACATTTATTGATGCAA
* * * *
28591449 ATGTCCCAGACGTGGTCTTACATGAAATCACATATATCGATGCCAACGTCCCAGACGTGGTCTTA
1 ATGTCCCAGACATGCTCTTACACGAAACCACATATATCGATGCCAACGTCCCAGACGTGGTCTTA
28591514 CACAAAATCACAT
66 CACAAAATCACAT
28591527 ATCAGAATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 72 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (90 bp):
ATGTCCCAGACATGCTCTTACACGAAACCACATATATCGATGCCAACGTCCCAGACGTGGTCTTA
CACAAAATCACATTTATTGATGCAA
Found at i:28592634 original size:14 final size:15
Alignment explanation
Indices: 28592617--28592645 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28592607 GCACGAAAAT
28592617 TTCACACAT-ATAAA
1 TTCACACATAATAAA
28592631 TTCACACATAATAAA
1 TTCACACATAATAAA
28592646 CACAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:28597067 original size:17 final size:19
Alignment explanation
Indices: 28597025--28597068 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
28597015 ATGAAATTTT
*
28597025 AATTAGTATTATAAGATAA
1 AATTATTATTATAAGATAA
*
28597044 AATTATTATTATTAGA-AA
1 AATTATTATTATAAGATAA
28597062 AA-TATTA
1 AATTATTA
28597069 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
AATTATTATTATAAGATAA
Found at i:28598232 original size:19 final size:20
Alignment explanation
Indices: 28598208--28598250 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28598198 TGTTTTGTTG
28598208 TGGG-CCAACTGTATTGAAA
1 TGGGCCCAACTGTATTGAAA
* *
28598227 TGGGCCCAACTGTGTTGATA
1 TGGGCCCAACTGTATTGAAA
28598247 TGGG
1 TGGG
28598251 TAAGGCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.23, C:0.16, G:0.33, T:0.28
Consensus pattern (20 bp):
TGGGCCCAACTGTATTGAAA
Found at i:28601627 original size:27 final size:27
Alignment explanation
Indices: 28601597--28601652 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
28601587 TGGAGGTTTA
* *
28601597 ATTTCTCTTGTAGTTCTATTTTTGGCG
1 ATTTCTCTTCTAGTTCTATTTTTAGCG
28601624 ATTTCTCTTCTAGTTCTATTTTTAGCG
1 ATTTCTCTTCTAGTTCTATTTTTAGCG
28601651 AT
1 AT
28601653 AGAGTATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.55
Consensus pattern (27 bp):
ATTTCTCTTCTAGTTCTATTTTTAGCG
Found at i:28604565 original size:17 final size:17
Alignment explanation
Indices: 28604543--28604578 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28604533 TAAAAAAGGG
28604543 TTTTATTTTTATTATCT
1 TTTTATTTTTATTATCT
28604560 TTTTATTTTTATTATCT
1 TTTTATTTTTATTATCT
28604577 TT
1 TT
28604579 CCTCTAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTATTTTTATTATCT
Found at i:28609678 original size:33 final size:33
Alignment explanation
Indices: 28609641--28609714 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
28609631 TGGCCTTACC
* * *
28609641 ATGGTCTTA-CATTCATAATGCCATAACTCAGTT
1 ATGGTCTTATCA-TCAGAATGCCATAACCCAGCT
* *
28609674 ATGGTCTTATCATCAGGATGCCATAGCCCAGCT
1 ATGGTCTTATCATCAGAATGCCATAACCCAGCT
28609707 ATGGTCTT
1 ATGGTCTT
28609715 GCACGTATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (33 bp):
ATGGTCTTATCATCAGAATGCCATAACCCAGCT
Found at i:28612535 original size:27 final size:27
Alignment explanation
Indices: 28612304--28612539 Score: 155
Period size: 27 Copynumber: 8.7 Consensus size: 27
28612294 GGATAGAATC
*
28612304 ACTGAAATACCCTTCG-TTTACAAAATT
1 ACTGAAATACCCTT-GATTTGCAAAATT
** *
28612331 A-TAGAAATACCCTTGACCTGTAAAATT
1 ACT-GAAATACCCTTGATTTGCAAAATT
* * * *
28612358 A-TCGAAATACCCCTAACTTGTAAAATT
1 ACT-GAAATACCCTTGATTTGCAAAATT
* * * *
28612385 ACTAAAATACCCTCGATTTGTAAAGTT
1 ACTGAAATACCCTTGATTTGCAAAATT
** *
28612412 ACCAAAATACCATTGATTTAG-AAAATT
1 ACTGAAATACCCTTGATTT-GCAAAATT
* * *
28612439 ACAGAAATACCCCTGATTTACAAAATT
1 ACTGAAATACCCTTGATTTGCAAAATT
28612466 A-TAGAAATA-CCTTGACTTT-CAAAAATT
1 ACT-GAAATACCCTTGA-TTTGC-AAAATT
* *
28612493 A-TAGAAATACCATTGGTTTGCAAAATT
1 ACT-GAAATACCCTTGATTTGCAAAATT
*
28612520 ACTGAAATACCCTTGGTTTG
1 ACTGAAATACCCTTGATTTG
28612540 TAGATTTACC
Statistics
Matches: 170, Mismatches: 28, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
26 8 0.05
27 154 0.91
28 8 0.05
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.31
Consensus pattern (27 bp):
ACTGAAATACCCTTGATTTGCAAAATT
Found at i:28612622 original size:27 final size:27
Alignment explanation
Indices: 28612592--28612683 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
28612582 ACCCCTAATA
*
28612592 GGTAAAAAGACCGTAATGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
*
28612619 GGTAAAATGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAATGCCCCTGTAG
* * * *
28612646 GG-AAGAGTGACCGTAATACCCTTGTAT
1 GGTAA-AATGACCGTAATGCCCCTGTAG
28612673 GGTAAAATGAC
1 GGTAAAATGAC
28612684 AATTATGCCC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.04
27 51 0.93
28 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.21
Consensus pattern (27 bp):
GGTAAAATGACCGTAATGCCCCTGTAG
Found at i:28612910 original size:27 final size:27
Alignment explanation
Indices: 28612851--28612903 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
28612841 CATTCGCCGT
28612851 TACTGGTGGCTATGCCACAATTACTGA
1 TACTGGTGGCTATGCCACAATTACTGA
* * *
28612878 TACTGGTGGCTTTGCGACATTTACTG
1 TACTGGTGGCTATGCCACAATTACTG
28612904 TTTCTGGCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (27 bp):
TACTGGTGGCTATGCCACAATTACTGA
Found at i:28613107 original size:33 final size:33
Alignment explanation
Indices: 28613064--28613140 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
28613054 ACATCTACTG
*
28613064 TATTGTTACTGAATAGGGCTTTGGCCCAAACTA
1 TATTGATACTGAATAGGGCTTTGGCCCAAACTA
*
28613097 TATTGATACTGAATAGGGCTTTGGCCCAGACTA
1 TATTGATACTGAATAGGGCTTTGGCCCAAACTA
*
28613130 TACTGATACTG
1 TATTGATACTG
28613141 TGTTATTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (33 bp):
TATTGATACTGAATAGGGCTTTGGCCCAAACTA
Found at i:28614620 original size:10 final size:10
Alignment explanation
Indices: 28614563--28614611 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
28614553 TTAAATTCTA
28614563 AAAGATAAAT
1 AAAGATAAAT
*
28614573 ACAGATAAAT
1 AAAGATAAAT
**
28614583 AAAGA-ATTT
1 AAAGATAAAT
28614592 AAAGATAAAT
1 AAAGATAAAT
28614602 AAAGATAAAT
1 AAAGATAAAT
28614612 GGAGATAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
9 7 0.22
10 25 0.78
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:28614646 original size:14 final size:13
Alignment explanation
Indices: 28614616--28614656 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
28614606 ATAAATGGAG
*
28614616 ATAAAAGCTAA-A
1 ATAAAATCTAATA
28614628 ATAAAATCTAAATA
1 ATAAAATCT-AATA
28614642 ATAAAATCTAATA
1 ATAAAATCTAATA
28614655 AT
1 AT
28614657 TATCCTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 8 0.31
13 8 0.31
14 10 0.38
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAAATCTAATA
Found at i:28616440 original size:29 final size:29
Alignment explanation
Indices: 28616398--28616498 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
28616388 CATGAAATTG
28616398 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
28616427 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
28616456 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
28616484 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
28616499 ACTTACTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:28629102 original size:29 final size:28
Alignment explanation
Indices: 28629066--28629143 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
28629056 TCATGAGATT
28629066 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
28629096 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
28629123 TGGCACTAAGTGTGCGTGGTT
1 -GGCACTAAGTGTGCG-GGTT
28629144 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.14, G:0.31, T:0.29
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:28629385 original size:144 final size:144
Alignment explanation
Indices: 28629125--28629393 Score: 502
Period size: 144 Copynumber: 1.9 Consensus size: 144
28629115 AAAGTACATG
*
28629125 GCACTAAGTGTGCGTGGTTGATTATTAAGCACTATGTGTGCGAACCCAATATATATTTTCTATAA
1 GCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTGCGAACCCAATATATATTTTCTATAA
*
28629190 ATTATTTACATGAAGGGTGCGACTTTACCGAGTTGATTTTGGACAGCGGAAAAGGTAAGTGTGCG
66 ATTATTTACATGAAGGGTGCGACTTTACCGAGTCGATTTTGGACAGCGGAAAAGGTAAGTGTGCG
28629255 AACTTGAAATGCAT
131 AACTTGAAATGCAT
*
28629269 GCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTGCGAACTCAATATATATTTTCTATAA
1 GCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTGCGAACCCAATATATATTTTCTATAA
*
28629334 ATTATTTACATTAAGGGTGCGACTTTACCGAGTCGATTTTGGACAGCGGAAAAGGTAAGT
66 ATTATTTACATGAAGGGTGCGACTTTACCGAGTCGATTTTGGACAGCGGAAAAGGTAAGT
28629394 ACCTTGAGTT
Statistics
Matches: 121, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
144 121 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (144 bp):
GCACTAAGTGTGCGCGGTTGATTATTAAGCACTATGTGTGCGAACCCAATATATATTTTCTATAA
ATTATTTACATGAAGGGTGCGACTTTACCGAGTCGATTTTGGACAGCGGAAAAGGTAAGTGTGCG
AACTTGAAATGCAT
Found at i:28631325 original size:96 final size:97
Alignment explanation
Indices: 28631163--28631344 Score: 258
Period size: 96 Copynumber: 1.9 Consensus size: 97
28631153 TATTTATTTA
* * * *
28631163 TTTATTTTTACTTAAGAATATGTTAAACCTTTTGATGCGAAGAGAGATAACAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCTCA
* * *
28631228 CCTCGGTTAGTCAGCCCAACATACTCCTAATT
66 CCCCAGTTACTCAGCCCAACATACTCCTAATT
* **
28631260 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGCGAAGAGAGATGGCAGCCAAGCACCTCA
1 TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCTCA
*
28631324 CCCCAGTTACTTAGCCCAACA
66 CCCCAGTTACTCAGCCCAACA
28631345 CATTCTTAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
96 65 0.88
97 9 0.12
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (97 bp):
TTTATTTTTACTTAAGAACATATCAAACCTTTTGACGCGAAGAGAGATAACAGCCAAGCACCTCA
CCCCAGTTACTCAGCCCAACATACTCCTAATT
Found at i:28640711 original size:28 final size:29
Alignment explanation
Indices: 28640654--28640711 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
28640644 TACAGAGGTT
*
28640654 TTCACAAGGCCAGGAACATGCCCGTGTCC
1 TTCACAAGGCCAGGAACACGCCCGTGTCC
* *
28640683 TTCACACGGCCATG-ACACGCCCGTGTCC
1 TTCACAAGGCCAGGAACACGCCCGTGTCC
28640711 T
1 T
28640712 AGCCTATGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.21, C:0.38, G:0.22, T:0.19
Consensus pattern (29 bp):
TTCACAAGGCCAGGAACACGCCCGTGTCC
Found at i:28643629 original size:27 final size:26
Alignment explanation
Indices: 28643585--28643636 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28643575 CTCGCTGCAA
*
28643585 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
28643612 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
28643637 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:28643704 original size:26 final size:27
Alignment explanation
Indices: 28643675--28643734 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
28643665 CCACATATAT
*
28643675 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
28643701 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
28643728 ATATCTG
1 ATATCTG
28643735 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:28648379 original size:6 final size:6
Alignment explanation
Indices: 28648368--28648419 Score: 86
Period size: 6 Copynumber: 8.5 Consensus size: 6
28648358 CAAACAAAGT
*
28648368 AATAAA AATAAA AAGCAAA AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AA-TAAA AATAAA AATAAA AATAAA AATAAA AATAAA
28648417 AAT
1 AAT
28648420 TGGGTTGCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
6 38 0.88
7 5 0.12
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:28648386 original size:25 final size:25
Alignment explanation
Indices: 28648368--28648419 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
28648358 CAAACAAAGT
28648368 AATAAAAATAAAAAGCAAAAATAAA
1 AATAAAAATAAAAAGCAAAAATAAA
*
28648393 AATAAAAATAAAAA-TAAAAATAAA
1 AATAAAAATAAAAAGCAAAAATAAA
28648417 AAT
1 AAT
28648420 TGGGTTGCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (25 bp):
AATAAAAATAAAAAGCAAAAATAAA
Found at i:28650975 original size:23 final size:23
Alignment explanation
Indices: 28650924--28650975 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
28650914 AAATTTCATT
*
28650924 GAATTGGTATAAACATGAGGATG
1 GAATTGGTATAAACATGAAGATG
*
28650947 GTATTGGTATAAA-ATGGATAGA-G
1 GAATTGGTATAAACAT-GA-AGATG
28650970 GAATTG
1 GAATTG
28650976 AGAATGTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
22 2 0.08
23 20 0.83
24 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.31, T:0.29
Consensus pattern (23 bp):
GAATTGGTATAAACATGAAGATG
Found at i:28657468 original size:41 final size:41
Alignment explanation
Indices: 28657410--28657557 Score: 149
Period size: 41 Copynumber: 3.6 Consensus size: 41
28657400 GAGCTTGGTC
28657410 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * *
28657451 TCGAAGGGCTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * * *
28657491 CCAAAGGGCCTTCGAGCCAGTGGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
* *
28657532 TGGAAGGGCTTTTGAGCCAGTACTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
28657558 GAATCGGGCT
Statistics
Matches: 86, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
39 4 0.05
40 33 0.38
41 46 0.53
43 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:28674944 original size:14 final size:13
Alignment explanation
Indices: 28674919--28674943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28674909 ACCTGGGAAA
28674919 AAAATAAAAAAAC
1 AAAATAAAAAAAC
28674932 AAAATAAAAAAA
1 AAAATAAAAAAA
28674944 AGACAGAATT
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:0.88, C:0.04, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATAAAAAAAC
Found at i:28674986 original size:17 final size:18
Alignment explanation
Indices: 28674966--28674999 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28674956 AAGTTGATTG
28674966 AAATTGC-AAAATTAAAT
1 AAATTGCAAAAATTAAAT
28674983 AAATTGCAAAAATTAAA
1 AAATTGCAAAAATTAAA
28675000 ATAGAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (18 bp):
AAATTGCAAAAATTAAAT
Found at i:28675606 original size:67 final size:67
Alignment explanation
Indices: 28675498--28675762 Score: 530
Period size: 67 Copynumber: 4.0 Consensus size: 67
28675488 CCTTTTTTTA
28675498 GGAATTTTTGACAACCTTTGGCTAGATGGATTTAGTGGCTCATGCTTTTGGGAAAAGAAATAGAT
1 GGAATTTTTGACAACCTTTGGCTAGATGGATTTAGTGGCTCATGCTTTTGGGAAAAGAAATAGAT
28675563 TG
66 TG
28675565 GGAATTTTTGACAACCTTTGGCTAGATGGATTTAGTGGCTCATGCTTTTGGGAAAAGAAATAGAT
1 GGAATTTTTGACAACCTTTGGCTAGATGGATTTAGTGGCTCATGCTTTTGGGAAAAGAAATAGAT
28675630 TG
66 TG
28675632 GGAATTTTTGACAACCTTTGGCTAGATGGATTTAGTGGCTCATGCTTTTGGGAAAAGAAATAGAT
1 GGAATTTTTGACAACCTTTGGCTAGATGGATTTAGTGGCTCATGCTTTTGGGAAAAGAAATAGAT
28675697 TG
66 TG
28675699 GGAATTTTTGACAACCTTTGGCTAGATGGATTTAGTGGCTCATGCTTTTGGGAAAAGAAATAGA
1 GGAATTTTTGACAACCTTTGGCTAGATGGATTTAGTGGCTCATGCTTTTGGGAAAAGAAATAGA
28675763 CTTAATAAAA
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 198 1.00
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.34
Consensus pattern (67 bp):
GGAATTTTTGACAACCTTTGGCTAGATGGATTTAGTGGCTCATGCTTTTGGGAAAAGAAATAGAT
TG
Found at i:28675944 original size:10 final size:10
Alignment explanation
Indices: 28675919--28675968 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
28675909 TTAACTTCTA
28675919 AAAGATAAA-
1 AAAGATAAAT
28675928 AATAGATAAAT
1 AA-AGATAAAT
**
28675939 AAAGATATTT
1 AAAGATAAAT
*
28675949 AAAAATAAAT
1 AAAGATAAAT
28675959 AAAGATAAAT
1 AAAGATAAAT
28675969 GGAGATAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:28676003 original size:14 final size:13
Alignment explanation
Indices: 28675973--28676013 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
28675963 ATAAATGGAG
*
28675973 ATAAAAGCTAA-A
1 ATAAAATCTAATA
28675985 ATAAAATCTAAATA
1 ATAAAATCT-AATA
28675999 ATAAAATCTAATA
1 ATAAAATCTAATA
28676012 AT
1 AT
28676014 TATCCTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 8 0.31
13 8 0.31
14 10 0.38
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (13 bp):
ATAAAATCTAATA
Found at i:28690525 original size:42 final size:42
Alignment explanation
Indices: 28690414--28690567 Score: 211
Period size: 42 Copynumber: 3.6 Consensus size: 42
28690404 TACCATACCA
* * **
28690414 ATGCCATATCCTAGATATGGTCTTACATGTAA-TCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTTATATCG
* *
28690456 ATGCCAATAGCCCAGCTATGGTCTTACACGAAGTCTTATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTTATATCG
*
28690499 ATGCCATATCCCAGATATGGTCTTACACGAAGCCTTATATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTTATATCG
*
28690541 ATGCCATATCCCAGATATGGTCATACA
1 ATGCCATATCCCAGATATGGTCTTACA
28690568 TGTAATCTTA
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
42 67 0.67
43 33 0.33
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTTATATCG
Found at i:28696423 original size:50 final size:50
Alignment explanation
Indices: 28696348--28696524 Score: 246
Period size: 50 Copynumber: 3.5 Consensus size: 50
28696338 CCATGGCAAC
*
28696348 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
28696398 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGAACAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
28696448 AAGTGACAAGTGATAGCTTCGGCTGCACTTATCTAATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
28696498 CAAGTGAAAAATGGTAGCTTCGACTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
28696525 CTGATCAGTG
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 90 0.81
51 21 0.19
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.24
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:28696538 original size:31 final size:31
Alignment explanation
Indices: 28696500--28696648 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
28696490 ACAAATGACA
* *
28696500 AGTGAAAAATGGTAGCTTCGACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
**
28696531 AGTGAAAAGTGGTAGCTTCTACTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28696562 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
28696593 AGTGAAAAATGGTAGCTCCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28696624 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
28696649 AAGTGACAAG
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:28696720 original size:46 final size:48
Alignment explanation
Indices: 28696670--28696834 Score: 150
Period size: 42 Copynumber: 3.6 Consensus size: 48
28696660 GATTTCCGTA
* * * *
28696670 TAAGACCATATCTAGGATATGGCATCA-GTGAGATATGTGATT-CGTG
1 TAAGACCATAGCTAGGCTATGGCATCATATGAGATATATGATTACGTG
* * *
28696716 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATATGCTTACGTG
1 TAAGACCATAGCTAGGCTATGGCATC-ATATGAGATATATGATTACGTG
* * *
28696765 TAAGACCATAGCTTGGCTATGGCATC-----A-ATATATGAATATGTG
1 TAAGACCATAGCTAGGCTATGGCATCATATGAGATATATGATTACGTG
*
28696807 TAAGACCATAGCT-GGCCTATGGGATCAT
1 TAAGACCATAGCTAGG-CTATGGCATCAT
28696835 TATGTGAAGA
Statistics
Matches: 100, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
41 2 0.02
42 34 0.34
46 23 0.23
47 1 0.01
48 11 0.11
49 29 0.29
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (48 bp):
TAAGACCATAGCTAGGCTATGGCATCATATGAGATATATGATTACGTG
Found at i:28696771 original size:49 final size:47
Alignment explanation
Indices: 28696670--28696841 Score: 153
Period size: 49 Copynumber: 3.7 Consensus size: 47
28696660 GATTTCCGTA
* * * * *
28696670 TAAGACCATATCTAGGATATGGCATCA-GTGAGATATGTGATTCGTG
1 TAAGACCATAGCTAGGCTATGGCATCATATGTGATATATGATTCGTG
* *
28696716 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATATGCTTACGTG
1 TAAGACCATAGCTAGGCTATGGCATC-ATATGTGATATATGATT-CGTG
* *
28696765 TAAGACCATAGCTTGGCTATGGCATCA-ATAT-ATGA-AT-A-T-GTG
1 TAAGACCATAGCTAGGCTATGGCATCATATGTGAT-ATATGATTCGTG
*
28696807 TAAGACCATAGCT-GGCCTATGGGATCATTATGTGA
1 TAAGACCATAGCTAGG-CTATGGCATCA-TATGTGA
28696842 AGATGTGTAA
Statistics
Matches: 106, Mismatches: 12, Indels: 17
0.79 0.09 0.13
Matches are distributed among these distances:
41 2 0.02
42 26 0.25
44 4 0.04
45 1 0.01
46 27 0.25
47 5 0.05
48 12 0.11
49 29 0.27
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (47 bp):
TAAGACCATAGCTAGGCTATGGCATCATATGTGATATATGATTCGTG
Found at i:28696809 original size:42 final size:42
Alignment explanation
Indices: 28696762--28696874 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 42
28696752 ATATGCTTAC
*
28696762 GTGTAAGACCATAGCTTGGCTATGGCATCAATATATGAATAT
1 GTGTAAGACCATAGCTTGGCTATGGCATCAATATATGAAGAT
* * *
28696804 GTGTAAGACCATAGC-TGGCCTATGGGATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTTGG-CTATGGCATCAATATATGAAGAT
*
28696846 GTGTAAGACCATA-TTTGAGCTATGGCATC
1 GTGTAAGACCATAGCTTG-GCTATGGCATC
28696875 GAGAAAACGA
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
41 3 0.05
42 58 0.94
43 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATAGCTTGGCTATGGCATCAATATATGAAGAT
Found at i:28697554 original size:115 final size:115
Alignment explanation
Indices: 28697416--28697645 Score: 424
Period size: 115 Copynumber: 2.0 Consensus size: 115
28697406 TGTGTATATA
28697416 TATGAGAAATTTAATGAGAATTGAGCCCATACATGTTTCTTGTTATTTATATGAAGTGTACGACT
1 TATGAGAAATTTAATGAGAATTGAGCCCATACATGTTTCTTGTTATTTATATGAAGTGTACGACT
* * * *
28697481 GACAAGGGTGATGAAGTTATAAACAGAGAGTTACACGGGTTGAAAACACG
66 GACAAGGATGATGAAGTTATAAACAAAGAGTTACACGAGTTAAAAACACG
28697531 TATGAGAAATTTAATGAGAATTGAGCCCATACATGTTTCTTGTTATTTATATGAAGTGTACGACT
1 TATGAGAAATTTAATGAGAATTGAGCCCATACATGTTTCTTGTTATTTATATGAAGTGTACGACT
28697596 GACAAGGATGATGAAGTTATAAACAAAGAGTTACACGAGTTAAAAACACG
66 GACAAGGATGATGAAGTTATAAACAAAGAGTTACACGAGTTAAAAACACG
28697646 GGCGAGTGAC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 111 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (115 bp):
TATGAGAAATTTAATGAGAATTGAGCCCATACATGTTTCTTGTTATTTATATGAAGTGTACGACT
GACAAGGATGATGAAGTTATAAACAAAGAGTTACACGAGTTAAAAACACG
Found at i:28708332 original size:50 final size:50
Alignment explanation
Indices: 28708257--28708433 Score: 264
Period size: 50 Copynumber: 3.5 Consensus size: 50
28708247 CCATGGCAAC
28708257 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * * *
28708307 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTAAACAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
28708357 AAGTGACAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
28708407 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
28708434 CTGATCAGTG
Statistics
Matches: 111, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 88 0.79
51 23 0.21
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:28708447 original size:31 final size:31
Alignment explanation
Indices: 28708409--28708588 Score: 272
Period size: 31 Copynumber: 5.8 Consensus size: 31
28708399 ACAAATGACA
28708409 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
28708440 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
28708471 AGTGAAAAGTGGTAGCTTCTGCTACCTGATA
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
28708502 AGTGAAAAGTGGTAGC-TCTGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTGATC
* * *
28708533 AGTGAAAAATGGTAGCTCCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* * *
28708564 AGTGAATAGTGATAGCTTCGACTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
28708589 AAGTGACAAG
Statistics
Matches: 135, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
30 2 0.01
31 132 0.98
32 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:28708758 original size:42 final size:42
Alignment explanation
Indices: 28708700--28708797 Score: 162
Period size: 42 Copynumber: 2.3 Consensus size: 42
28708690 TTTGTGATTC
*
28708700 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATATGAAGAT
*
28708742 GTGTAAGACCATAGCTGGGCTATGGCATCATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCATTATATGAAGAT
28708784 GTGTAAGACCATAG
1 GTGTAAGACCATAG
28708798 TTGACCGATG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCATTATATGAAGAT
Found at i:28712946 original size:27 final size:27
Alignment explanation
Indices: 28712915--28713120 Score: 234
Period size: 27 Copynumber: 7.6 Consensus size: 27
28712905 TAAATTGTAC
28712915 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
28712942 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
28712968 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
28712996 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
28713024 AGCACTAAGTGTGCGATTTGACTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* *
28713051 GGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
28713079 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
28713106 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28713121 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
27 106 0.70
28 46 0.30
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:28713030 original size:82 final size:82
Alignment explanation
Indices: 28712914--28713120 Score: 256
Period size: 82 Copynumber: 2.5 Consensus size: 82
28712904 TTAAATTGTA
* * *
28712914 CAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAG
1 CAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAG
28712978 TGTGCGA-ATTGACCATG
65 TGTGCGAGATTGACCATG
* ** *
28712995 CGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGACTACGTGGCACTAAG
1 CAGCACTAAGTGTGCGAGT-TGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAG
* **
28713060 TGTGCGAGTTTGATTATG
65 TGTGCGAGATTGACCATG
* * * *
28713078 TAGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 CAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
28713121 GACTTAATAT
Statistics
Matches: 108, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
81 18 0.17
82 66 0.61
83 24 0.22
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (82 bp):
CAGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGT
GTGCGAGATTGACCATG
Found at i:28713045 original size:55 final size:55
Alignment explanation
Indices: 28712915--28713120 Score: 254
Period size: 55 Copynumber: 3.8 Consensus size: 55
28712905 TAAATTGTAC
* *
28712915 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGA-AATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTATGAATATGT
* * * * *
28712968 ATGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCTGACTATGT
1 A-GCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTATGAATATGT
* * *
28713024 AGCACTAAGTGTGCGATTTGACTACGTGGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTATGAATATGT
* * * * *
28713079 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCG
28713121 GACTTAATAT
Statistics
Matches: 131, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 38 0.29
55 91 0.69
56 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.30
Consensus pattern (55 bp):
AGCACTAAGTGTGCGATTTGACTATGTGGCACTAAGTGTGCGAGTATGAATATGT
Found at i:28720937 original size:39 final size:40
Alignment explanation
Indices: 28720842--28721064 Score: 273
Period size: 39 Copynumber: 5.7 Consensus size: 40
28720832 TTGAATGATG
*
28720842 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28720880 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
28720921 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28720960 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28720999 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28721038 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28721065 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
39 93 0.56
40 61 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28721028 original size:79 final size:81
Alignment explanation
Indices: 28720842--28721064 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
28720832 TTGAATGATG
* * *
28720842 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATATCCGGGCTAAGACCCGAAGGCA
*
28720903 TTTGTGCGAGATACTAAT
64 TTTGTGCGAGATACTAAA
28720921 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
*
28720983 TGTGCGAGTTACTAAA
66 TGTGCGAGATACTAAA
* * * * *
28720999 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
28721063 TG
66 TG
28721065 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:28721086 original size:79 final size:79
Alignment explanation
Indices: 28720842--28721097 Score: 224
Period size: 79 Copynumber: 3.3 Consensus size: 79
28720832 TTGAATGATG
* * * *
28720842 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
28720903 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
28720921 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
28720985 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
28720999 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATT
*
28721063 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
28721079 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28721098 TACGTGATTT
Statistics
Matches: 153, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
77 1 0.01
78 45 0.29
79 70 0.46
80 36 0.24
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:28732594 original size:18 final size:18
Alignment explanation
Indices: 28732571--28732612 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28732561 GAACAATTAT
*
28732571 TTATTCAGAATCAGTCTG
1 TTATTCAGAATCAGTCAG
* *
28732589 TTATTCGGTATCAGTCAG
1 TTATTCAGAATCAGTCAG
28732607 TTATTC
1 TTATTC
28732613 GGTAACAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.43
Consensus pattern (18 bp):
TTATTCAGAATCAGTCAG
Found at i:28732613 original size:18 final size:18
Alignment explanation
Indices: 28732580--28732630 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
28732570 TTTATTCAGA
*
28732580 ATCAGTCTGTTATTCGGT
1 ATCAGTCAGTTATTCGGT
28732598 ATCAGTCAGTTATTCGGT
1 ATCAGTCAGTTATTCGGT
* * *
28732616 AACAATCAATTATTC
1 ATCAGTCAGTTATTC
28732631 AATACTAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (18 bp):
ATCAGTCAGTTATTCGGT
Found at i:28732640 original size:18 final size:18
Alignment explanation
Indices: 28732618--28732662 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
28732608 TATTCGGTAA
28732618 CAATCAATTATTCAATA-
1 CAATCAATTATTCAATAT
* *
28732635 CTAATCAGTTATTCAGTAT
1 C-AATCAATTATTCAATAT
28732654 CAATCAATT
1 CAATCAATT
28732663 GATCGGTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (18 bp):
CAATCAATTATTCAATAT
Found at i:28732695 original size:18 final size:18
Alignment explanation
Indices: 28732669--28732744 Score: 71
Period size: 18 Copynumber: 4.1 Consensus size: 18
28732659 AATTGATCGG
*
28732669 TTATCCAGTAACAATCAA
1 TTATTCAGTAACAATCAA
*
28732687 TTATTCAGTAAAAATCAGA
1 TTATTCAGTAACAATCA-A
* * *
28732706 TATATACAGTGACAATTAAA
1 T-TATTCAGTAACAA-TCAA
*
28732726 TTATTCAGTAACAGTCAA
1 TTATTCAGTAACAATCAA
28732744 T
1 T
28732745 CTTTCCAGTT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
18 19 0.42
19 12 0.27
20 12 0.27
21 2 0.04
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:28732979 original size:53 final size:53
Alignment explanation
Indices: 28732860--28732984 Score: 151
Period size: 53 Copynumber: 2.4 Consensus size: 53
28732850 CTGGAACAAT
* * * * *
28732860 AACAGTAACAGTAGCAATATGGTACACAGAGTACCTCATCAGAATAAATCCGG
1 AACAGTAACAGTAACAATACGGTACACAAAGTACCTCATCAGAACAAATCCGA
* * ** *
28732913 AACGGTAACAGTAACAGTACGGTACACAAAGTACCTCATTGGAACAAATTCGA
1 AACAGTAACAGTAACAATACGGTACACAAAGTACCTCATCAGAACAAATCCGA
*
28732966 AACAGTAATAGTAACAATA
1 AACAGTAACAGTAACAATA
28732985 TCCGACACAC
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (53 bp):
AACAGTAACAGTAACAATACGGTACACAAAGTACCTCATCAGAACAAATCCGA
Found at i:28735079 original size:11 final size:11
Alignment explanation
Indices: 28735063--28735118 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
28735053 AATGATTGAT
28735063 ATGATATGCAC
1 ATGATATGCAC
*
28735074 ATGATATG--T
1 ATGATATGCAC
28735083 ATGATATGCAC
1 ATGATATGCAC
*
28735094 ATGATATGTAC
1 ATGATATGCAC
*
28735105 --GAAATGCAC
1 ATGATATGCAC
28735114 ATGAT
1 ATGAT
28735119 GAATTCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:28735085 original size:20 final size:20
Alignment explanation
Indices: 28735062--28735118 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
28735052 AAATGATTGA
28735062 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
28735082 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
* *
28735102 TACGAAATGCACATGAT
1 TATGATATGCACATGAT
28735119 GAATTCATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:28735259 original size:25 final size:26
Alignment explanation
Indices: 28735168--28735290 Score: 178
Period size: 26 Copynumber: 4.8 Consensus size: 26
28735158 GAGGAAGTGC
*
28735168 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCA
*
28735194 AAAAGAGCTTATGCCCCAGTTTACCA
1 AAAAGGGCTTATGCCCCAGTTTACCA
**
28735220 AAAAGGGCTTATGCCCCAGTTTATTA
1 AAAAGGGCTTATGCCCCAGTTTACCA
*
28735246 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCA
*
28735271 AAAAGGGCTT-TACCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28735291 ATTAAAGAGG
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
25 31 0.35
26 57 0.65
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCA
Found at i:28735493 original size:42 final size:42
Alignment explanation
Indices: 28735434--28735526 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
28735424 GTAGTCTCCC
*
28735434 CAAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATT
1 CAAATGGGCTTGCATACATTCATTGATATTTCATGTGATATT
*
28735476 CAAATGGGCTTGCATACATTCATTGATATTTCATGTGTTATT
1 CAAATGGGCTTGCATACATTCATTGATATTTCATGTGATATT
*
28735518 GAAATGGGC
1 CAAATGGGC
28735527 CTATGGGCCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (42 bp):
CAAATGGGCTTGCATACATTCATTGATATTTCATGTGATATT
Found at i:28735585 original size:31 final size:31
Alignment explanation
Indices: 28735550--28735628 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
28735540 CATTTACAAT
*
28735550 AAAGGCTTTGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
28735581 AAAGGCTTCGGCCCAGTGATTTGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
28735612 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
28735629 AACCGTTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:28742181 original size:40 final size:39
Alignment explanation
Indices: 28742150--28742359 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
28742140 GGACTAAGAT
* *
28742150 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
28742190 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
28742230 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
28742270 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
28742310 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
28742349 CCGAAGGCATT
1 CCGAAGGCATT
28742360 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:28742313 original size:120 final size:120
Alignment explanation
Indices: 28742097--28742359 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
28742087 TTGAATGCTG
* *
28742097 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
28742161 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
28742217 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
28742280 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
28742336 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28742360 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28742379 original size:79 final size:80
Alignment explanation
Indices: 28742098--28742394 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
28742088 TGAATGCTGT
* ** * * * **
28742098 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
28742161 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
28742178 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
28742242 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
28742258 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
28742322 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
28742337 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
28742395 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:28750177 original size:40 final size:40
Alignment explanation
Indices: 28750088--28750387 Score: 423
Period size: 40 Copynumber: 7.5 Consensus size: 40
28750078 TTGAATGCTG
* * *
28750088 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
** * *
28750127 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28750167 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
28750206 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
28750246 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
28750286 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28750326 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
28750367 -CCGGGCTATGTCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCA
28750388 CTTGAACGAG
Statistics
Matches: 242, Mismatches: 12, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
39 53 0.22
40 179 0.74
41 10 0.04
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28750409 original size:120 final size:120
Alignment explanation
Indices: 28750088--28750424 Score: 386
Period size: 120 Copynumber: 2.8 Consensus size: 120
28750078 TTGAATGCTG
* * * *
28750088 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAA-TTACTAA-ATCCGGGCTAAG-TCCCGAAGGCA
* ** * *
28750149 TTTGTGCGAGAT-ACTAATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
63 CTTGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
28750206 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCACTT
** *
28750271 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
66 GAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
28750326 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATGTCCCGAAGGCACT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTA-AATCCGGGCTAAGTCCCGAAGGCACT
* * *
28750390 TGAACGAG-GAGCTATATCC-GGTTAAATTCCGAAGG
65 TGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
28750425 TACGTGATTT
Statistics
Matches: 193, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
118 22 0.11
119 62 0.32
120 107 0.55
121 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (120 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAATCCGGGCTAAGTCCCGAAGGCACTT
GAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28752371 original size:18 final size:18
Alignment explanation
Indices: 28752350--28752405 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
28752340 TATCAGTTAG
* *
28752350 TTATTCGGTAACAATCAA
1 TTATTCAGTAATAATCAA
* *
28752368 TTATTCAATAATAATCAG
1 TTATTCAGTAATAATCAA
*
28752386 TTATTCAGTATTAATCAA
1 TTATTCAGTAATAATCAA
28752404 TT
1 TT
28752406 GATCGGTTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.41
Consensus pattern (18 bp):
TTATTCAGTAATAATCAA
Found at i:28752438 original size:18 final size:18
Alignment explanation
Indices: 28752412--28752485 Score: 69
Period size: 18 Copynumber: 4.1 Consensus size: 18
28752402 AATTGATCGG
*
28752412 TTATCCAGTAACAATCAA
1 TTATTCAGTAACAATCAA
*
28752430 TTATTCAGTAAAAATCAGA
1 TTATTCAGTAACAATCA-A
* * *
28752449 -TATACGGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
*
28752467 TTATTCAGTAACAGTCAA
1 TTATTCAGTAACAATCAA
28752485 T
1 T
28752486 CTTTCCAGTT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
18 30 0.70
19 13 0.30
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:28752715 original size:53 final size:53
Alignment explanation
Indices: 28752601--28752722 Score: 136
Period size: 53 Copynumber: 2.3 Consensus size: 53
28752591 CTGGAACAGT
* * * * *
28752601 AACAGTAACAATAGCAGTACAGTACACAGAGCACCTCATTAGAATAAATCCGG
1 AACAGTAACAATAACAGTACAGTACACAAAGCACCTCATCAGAACAAATCCGA
** * * * *
28752654 AATGGTAACAATAACAGTACGGTACACAAAGTACCTTATCGGAACAAATCCGA
1 AACAGTAACAATAACAGTACAGTACACAAAGCACCTCATCAGAACAAATCCGA
*
28752707 AACAGTAACAGTAACA
1 AACAGTAACAATAACA
28752723 ATATCCGACA
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.17
Consensus pattern (53 bp):
AACAGTAACAATAACAGTACAGTACACAAAGCACCTCATCAGAACAAATCCGA
Found at i:28752921 original size:16 final size:16
Alignment explanation
Indices: 28752892--28752925 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
28752882 TAATTCACTT
28752892 TTCAATTTTCAATTAA
1 TTCAATTTTCAATTAA
28752908 TTCATATTTT-AATTAA
1 TTCA-ATTTTCAATTAA
28752924 TT
1 TT
28752926 AACTATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCAATTTTCAATTAA
Found at i:28753822 original size:30 final size:28
Alignment explanation
Indices: 28753764--28753822 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 28
28753754 TAATTTAATG
*
28753764 ATAATAAATACATTAATTTTACTTAAATA
1 ATAATAAATACATCAATTTTAC-TAAATA
28753793 ATAAGTAAATACATGCATATTTTAC-AAATA
1 ATAA-TAAATACAT-CA-ATTTTACTAAATA
28753823 TATGTACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
29 4 0.15
30 14 0.54
31 1 0.04
32 7 0.27
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.37
Consensus pattern (28 bp):
ATAATAAATACATCAATTTTACTAAATA
Found at i:28757242 original size:32 final size:32
Alignment explanation
Indices: 28757198--28757267 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
28757188 AACCTTAATA
28757198 GGAAAATCCAATGGGACAAAACCTCGGTTAAG
1 GGAAAATCCAATGGGACAAAACCTCGGTTAAG
28757230 GGAAAA-CTCAATGGGACAAAACCTCGGTTAAG
1 GGAAAATC-CAATGGGACAAAACCTCGGTTAAG
28757262 GGAAAA
1 GGAAAA
28757268 AGAGTACAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 1 0.03
32 36 0.97
ACGTcount: A:0.43, C:0.17, G:0.26, T:0.14
Consensus pattern (32 bp):
GGAAAATCCAATGGGACAAAACCTCGGTTAAG
Found at i:28759187 original size:18 final size:18
Alignment explanation
Indices: 28759164--28759205 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
28759154 ATGCCAAGTG
28759164 GTAAACGCATTTGTATTA
1 GTAAACGCATTTGTATTA
28759182 GTAAACGCATTTGTATTA
1 GTAAACGCATTTGTATTA
28759200 GTAAAC
1 GTAAAC
28759206 TTCTAGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (18 bp):
GTAAACGCATTTGTATTA
Found at i:28761046 original size:33 final size:33
Alignment explanation
Indices: 28761007--28761072 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
28760997 TAGTTTTAGG
*
28761007 TTAATTTTTTTATCTGATTTTTCAAAATCGTGA
1 TTAATTTTTTTATCTAATTTTTCAAAATCGTGA
28761040 TTAATTTTTTTATCTAATTTTTCAAAATCGTGA
1 TTAATTTTTTTATCTAATTTTTCAAAATCGTGA
28761073 AACTAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.55
Consensus pattern (33 bp):
TTAATTTTTTTATCTAATTTTTCAAAATCGTGA
Found at i:28761640 original size:27 final size:27
Alignment explanation
Indices: 28761609--28761663 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
28761599 ATTCAATTTA
*
28761609 ATTTTGATTCTAACT-TTTTTACTTTT
1 ATTTTTATTCTAACTATTTTTACTTTT
* *
28761635 ATTTTTATTTTAATTATTTTTACTTTT
1 ATTTTTATTCTAACTATTTTTACTTTT
28761662 AT
1 AT
28761664 CAAAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.69
Consensus pattern (27 bp):
ATTTTTATTCTAACTATTTTTACTTTT
Found at i:28761653 original size:15 final size:16
Alignment explanation
Indices: 28761633--28761662 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28761623 TTTTTTACTT
28761633 TTATTTTTA-TTTTAA
1 TTATTTTTACTTTTAA
28761648 TTATTTTTACTTTTA
1 TTATTTTTACTTTTA
28761663 TCAAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTTACTTTTAA
Found at i:28762119 original size:25 final size:25
Alignment explanation
Indices: 28762080--28762127 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
28762070 ACAAAAATTG
* *
28762080 TTTTAAAAATTAAAAGTTTTTTTTTA
1 TTTTAAAAA-TAAAAATATTTTTTTA
28762106 TTTT-AAAATAAAAATATTTTTT
1 TTTTAAAAATAAAAATATTTTTT
28762128 GAACAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 12 0.60
25 4 0.20
26 4 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TTTTAAAAATAAAAATATTTTTTTA
Found at i:28765945 original size:43 final size:42
Alignment explanation
Indices: 28765888--28766050 Score: 177
Period size: 43 Copynumber: 3.8 Consensus size: 42
28765878 CAATGCCAAC
* * * *
28765888 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGTTGCCATT
1 GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCCA-T
28765931 GTCCCAGACATGGTCTTACACGAAATCAAATA-CGATGCCGAT
1 GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCC-AT
* * *
28765973 GTCCCAAACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC
1 GTCCCAGACATGGTCTTACACG-AAATC-AAATATCGATGCC-AT
* * *
28766017 ATCCCAGACGTGGTCTTACACGAAATCACATATC
1 GTCCCAGACATGGTCTTACACGAAATCAAATATC
28766051 AAAAATCCTA
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
42 29 0.28
43 44 0.43
44 29 0.28
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (42 bp):
GTCCCAGACATGGTCTTACACGAAATCAAATATCGATGCCAT
Found at i:28768155 original size:19 final size:20
Alignment explanation
Indices: 28768120--28768160 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
28768110 GGTTAATTTC
28768120 ATCTAAAATCGATTAAAAATA
1 ATCTAAAATC-ATTAAAAATA
28768141 ATCTAAAAT-ATTAAAAATA
1 ATCTAAAATCATTAAAAATA
28768160 A
1 A
28768161 ATAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
21 9 0.45
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (20 bp):
ATCTAAAATCATTAAAAATA
Found at i:28768168 original size:17 final size:19
Alignment explanation
Indices: 28768131--28768169 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28768121 TCTAAAATCG
*
28768131 ATTAAAAATAATCTAAAAT
1 ATTAAAAATAATATAAAAT
28768150 ATTAAAAATAA-AT-AAAT
1 ATTAAAAATAATATAAAAT
28768167 ATT
1 ATT
28768170 TTCAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 1 0.05
19 11 0.58
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAATAATATAAAAT
Found at i:28769730 original size:13 final size:14
Alignment explanation
Indices: 28769704--28769735 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
28769694 CGAAATAGGG
28769704 AGAAA-AAAAGGAA
1 AGAAAGAAAAGGAA
28769717 AGAAAGAAAA-GAA
1 AGAAAGAAAAGGAA
28769730 AGAAAG
1 AGAAAG
28769736 GAGAAACTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAAGGAA
Found at i:28772476 original size:26 final size:26
Alignment explanation
Indices: 28772447--28772606 Score: 266
Period size: 26 Copynumber: 6.2 Consensus size: 26
28772437 TGGTACAAAT
28772447 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
28772473 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28772499 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
28772525 TGATAATAGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28772551 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
28772577 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
28772603 TGAT
1 TGAT
28772607 GGGCATTTCA
Statistics
Matches: 123, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 123 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:28772509 original size:52 final size:52
Alignment explanation
Indices: 28772447--28772606 Score: 293
Period size: 52 Copynumber: 3.1 Consensus size: 52
28772437 TGGTACAAAT
28772447 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
*
28772499 TGATAATGGGTTAGGTAAATGTTCCATGATAATAGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
* *
28772551 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
28772603 TGAT
1 TGAT
28772607 GGGCATTTCA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 104 1.00
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (52 bp):
TGATAATGGGTTAGGTAAATGTTCCATGATAATGGATTAGGTAAATATTCCA
Found at i:28773798 original size:8 final size:8
Alignment explanation
Indices: 28773785--28773814 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
28773775 AGATCGGCAC
28773785 AAGCCGAA
1 AAGCCGAA
28773793 AAGCCGAA
1 AAGCCGAA
*
28773801 ATGCCGAA
1 AAGCCGAA
28773809 AAGCCG
1 AAGCCG
28773815 GTATTTTGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.27, G:0.27, T:0.03
Consensus pattern (8 bp):
AAGCCGAA
Found at i:28774304 original size:27 final size:27
Alignment explanation
Indices: 28774207--28774311 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
28774197 AGGAAGCGTC
*
28774207 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
28774234 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
28774261 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
28774288 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
28774312 GCAGCCTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:28776757 original size:17 final size:17
Alignment explanation
Indices: 28776735--28776770 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28776725 TTCATCTCAT
28776735 AATTCTATCATCATGCC
1 AATTCTATCATCATGCC
28776752 AATTCTATCATCATGCC
1 AATTCTATCATCATGCC
28776769 AA
1 AA
28776771 AGAGTTTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.06, T:0.33
Consensus pattern (17 bp):
AATTCTATCATCATGCC
Found at i:28782643 original size:27 final size:27
Alignment explanation
Indices: 28782613--28782790 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28782603 ATATTGAGTC
* * * *
28782613 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28782640 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28782667 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28782695 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28782722 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28782749 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28782776 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28782791 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28782752 original size:82 final size:81
Alignment explanation
Indices: 28782634--28782789 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28782624 TGCTATATAA
* *
28782634 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28782699 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28782716 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28782780 CACTTAGTGC
65 CACTTAGTGC
28782790 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28793221 original size:14 final size:14
Alignment explanation
Indices: 28793202--28793228 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28793192 AGAAATGTGA
28793202 AATTTAAATTTTTG
1 AATTTAAATTTTTG
28793216 AATTTAAATTTTT
1 AATTTAAATTTTT
28793229 AAAAAGCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
AATTTAAATTTTTG
Found at i:28800113 original size:22 final size:18
Alignment explanation
Indices: 28800071--28800106 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
28800061 TACAAATCAA
28800071 AATTGGATTGAGTCTCTC
1 AATTGGATTGAGTCTCTC
28800089 AATTGGATTGAGTCTCTC
1 AATTGGATTGAGTCTCTC
28800107 TTTCAATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (18 bp):
AATTGGATTGAGTCTCTC
Found at i:28804184 original size:25 final size:25
Alignment explanation
Indices: 28804150--28804205 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
28804140 TTCCTTATAA
**
28804150 ACTTTAAATTAAGAATTCTATTAGG
1 ACTTTAAATTAAGAATTAGATTAGG
*
28804175 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAAGAATTAGATTAGG
*
28804200 ATTTTA
1 ACTTTA
28804206 CTTTATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.41
Consensus pattern (25 bp):
ACTTTAAATTAAGAATTAGATTAGG
Found at i:28806918 original size:40 final size:40
Alignment explanation
Indices: 28806856--28807037 Score: 269
Period size: 40 Copynumber: 4.6 Consensus size: 40
28806846 TATTCGGATG
* * *
28806856 ATATCCGGGCTAAATCCTGAAGGCCTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
28806896 ATATCCGGGCTAAGTCCCGAAGGCCTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
28806936 ATATCCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
28806976 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
28807016 ATATCC-GGCTAATTCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
28807038 TACTTGGGTT
Statistics
Matches: 132, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 14 0.11
40 116 0.88
41 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:28813833 original size:40 final size:40
Alignment explanation
Indices: 28813778--28813959 Score: 242
Period size: 40 Copynumber: 4.6 Consensus size: 40
28813768 TATTCGGATG
* *
28813778 ATATCCGAGCTAAGTCCCGAAGGCCTTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
28813818 ATATCCGGGCTAAGTCTCGAAGACATTTATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
28813858 ATATCCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
28813898 ATATCCCGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
* *
28813938 ATAT-CTGGCTAATTCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
28813960 TACTTGGGTT
Statistics
Matches: 125, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
39 15 0.12
40 108 0.86
41 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:28829761 original size:21 final size:21
Alignment explanation
Indices: 28829737--28829780 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
28829727 GTAACATTAA
28829737 ACTAAAGATTAAAGAGTGATT
1 ACTAAAGATTAAAGAGTGATT
*
28829758 ACTAAAGATTAAATAGTGATT
1 ACTAAAGATTAAAGAGTGATT
28829779 AC
1 AC
28829781 AACTACTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.30
Consensus pattern (21 bp):
ACTAAAGATTAAAGAGTGATT
Found at i:28842673 original size:16 final size:15
Alignment explanation
Indices: 28842652--28842686 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
28842642 TCATAAACTG
28842652 AAATAAAAAATATAAA
1 AAATAAAAAATA-AAA
28842668 AAATAAAAAATAAAA
1 AAATAAAAAATAAAA
28842683 AAAT
1 AAAT
28842687 TGAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAAAATAAAA
Found at i:28843354 original size:35 final size:35
Alignment explanation
Indices: 28843308--28843377 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
28843298 TCTCTCGGCC
28843308 TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
1 TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
28843343 TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
1 TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
28843378 CCTAGTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (35 bp):
TCGTTTATCCTTGATTTCTTCCTAGGGTTGTCAAT
Found at i:28847612 original size:16 final size:16
Alignment explanation
Indices: 28847573--28847631 Score: 68
Period size: 16 Copynumber: 3.7 Consensus size: 16
28847563 AATTTCCCAT
*
28847573 TTTCTTTCTTT-TCTCC
1 TTTCTTTCTTTCTCT-A
28847589 TTTCTTTCTTTC-CTA
1 TTTCTTTCTTTCTCTA
*
28847604 TTTCGTTTCATTCTCTA
1 TTTC-TTTCTTTCTCTA
28847621 TTTCTTTCTTT
1 TTTCTTTCTTT
28847632 ATCTTTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
15 4 0.11
16 26 0.70
17 7 0.19
ACGTcount: A:0.05, C:0.25, G:0.02, T:0.68
Consensus pattern (16 bp):
TTTCTTTCTTTCTCTA
Found at i:28849656 original size:30 final size:30
Alignment explanation
Indices: 28849622--28849682 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28849612 TCCTTAACTC
28849622 AAACTTTTGAAAAATTACAATTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
* * * *
28849652 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
28849682 A
1 A
28849683 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:28857892 original size:25 final size:25
Alignment explanation
Indices: 28857839--28857951 Score: 90
Period size: 25 Copynumber: 4.6 Consensus size: 25
28857829 TTACCGATTG
*
28857839 CAGCTCGTGA-GAGCTTAC-AATTCT
1 CAGCTCGT-ATGAGCTTACTGATTCT
*
28857863 CAGCTCGTATGTGCTTACTGATTCT
1 CAGCTCGTATGAGCTTACTGATTCT
* * *
28857888 TAGCTTGTATGAGCTTACTGGTT-T
1 CAGCTCGTATGAGCTTACTGATTCT
* * * *
28857912 ACAGCTCGTGA-AAGCATACTAATTCA
1 -CAGCTCGT-ATGAGCTTACTGATTCT
28857938 CAGCTCGTATGAGC
1 CAGCTCGTATGAGC
28857952 ATACATGTAC
Statistics
Matches: 69, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
23 1 0.01
24 17 0.25
25 50 0.72
26 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACTGATTCT
Found at i:28863511 original size:44 final size:42
Alignment explanation
Indices: 28863441--28863598 Score: 131
Period size: 44 Copynumber: 3.7 Consensus size: 42
28863431 ATGTGTTATT
** * *
28863441 GTGTAAGACCACGTCTAAGACGTTGGCACCGACTTTTATTTCAC
1 GTGTAAGACCACGTCTGGGACATTGGCATCGA-TTTTATTT-AC
* * *
28863485 GTGTAAGACCATGTCTGGGACATTGGCATCGTATCTGATTT-C
1 GTGTAAGACCACGTCTGGGACATTGGCATCG-ATTTTATTTAC
* * * *
28863527 GTGTAAGACC-CTCTCTGGGATAGTGGCATCGATGTTTAATTAC
1 GTGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TTTATTTAC
* * *
28863570 ATGTAAGACCACATCTGGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACATTGGCAT
28863599 TGTATATGCT
Statistics
Matches: 90, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
41 2 0.02
42 31 0.34
43 23 0.26
44 33 0.37
45 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCACGTCTGGGACATTGGCATCGATTTTATTTAC
Found at i:28874292 original size:2 final size:2
Alignment explanation
Indices: 28874279--28874326 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
28874269 CTAACGAATA
*
28874279 TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28874321 TG TG TG
1 TG TG TG
28874327 AGAGAGAGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28878842 original size:3 final size:3
Alignment explanation
Indices: 28878834--28878858 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28878824 AGAATTTTTC
28878834 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
28878859 GCATAGCGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:28881120 original size:3 final size:3
Alignment explanation
Indices: 28881112--28881145 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28881102 AAATGTATAT
28881112 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28881146 AGAAAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28881646 original size:7 final size:7
Alignment explanation
Indices: 28881634--28881673 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
28881624 TAAAAAATTA
*
28881634 AATATTT
1 AATATTC
*
28881641 AATATTT
1 AATATTC
28881648 AATATTC
1 AATATTC
28881655 AATATTC
1 AATATTC
28881662 AATATTC
1 AATATTC
28881669 AATAT
1 AATAT
28881674 GAAATTGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (7 bp):
AATATTC
Found at i:28885477 original size:22 final size:22
Alignment explanation
Indices: 28885446--28885487 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28885436 CTTTATTCCT
* *
28885446 AATTTCTATATATTAATAAAGG
1 AATTTATATAGATTAATAAAGG
28885468 AATTTATATAGATTAATAAA
1 AATTTATATAGATTAATAAA
28885488 TTAGCATGAG
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:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
AATTTATATAGATTAATAAAGG
Done.