Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008670.1 Hibiscus syriacus cultivar Beakdansim tig00111678_pilon, whole genome shotgun sequence
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: 969061
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 5
Found at i:210939 original size:12 final size:12
Alignment explanation
Indices: 210922--210962 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
210912 ATACTATGCA
210922 AATAGTATCGTG
1 AATAGTATCGTG
*
210934 AATAGTA--ATG
1 AATAGTATCGTG
*
210944 AACAGTATCGTG
1 AATAGTATCGTG
210956 AATAGTA
1 AATAGTA
210963 ATGAACAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 8 0.35
12 15 0.65
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (12 bp):
AATAGTATCGTG
Found at i:210953 original size:22 final size:22
Alignment explanation
Indices: 210925--210979 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
210915 CTATGCAAAT
210925 AGTATCGTGAATAGTAATGAAC
1 AGTATCGTGAATAGTAATGAAC
210947 AGTATCGTGAATAGTAATGAAC
1 AGTATCGTGAATAGTAATGAAC
*
210969 AGTACCGTGAA
1 AGTATCGTGAA
210980 CAGTGATCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (22 bp):
AGTATCGTGAATAGTAATGAAC
Found at i:212044 original size:32 final size:32
Alignment explanation
Indices: 211976--212096 Score: 185
Period size: 32 Copynumber: 3.8 Consensus size: 32
211966 GAAAGACCAA
* *
211976 TCCATATGTTCCGAAGAACATAGGTAA--CTG
1 TCCATATGTCCCAAAGAACATAGGTAATCCTG
212006 TCCATATGTCCCAAAGAACATAGGTAATCCTG
1 TCCATATGTCCCAAAGAACATAGGTAATCCTG
*
212038 TCCATATGTCCCAAAGGACATAGGTAATCCTG
1 TCCATATGTCCCAAAGAACATAGGTAATCCTG
212070 TCCATATGTCCCGAAAG-ACATAGGTAA
1 TCCATATGTCCC-AAAGAACATAGGTAA
212097 CCCTCGACTC
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
30 25 0.29
32 56 0.66
33 4 0.05
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (32 bp):
TCCATATGTCCCAAAGAACATAGGTAATCCTG
Found at i:217168 original size:21 final size:21
Alignment explanation
Indices: 217144--217185 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
217134 AGTTTATTTT
217144 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
217165 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
217186 AACTTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:217233 original size:33 final size:33
Alignment explanation
Indices: 217180--217278 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
217170 TTTGTTTCAA
217180 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
217212 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
217245 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
217278 T
1 T
217279 ATGCTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:217307 original size:13 final size:13
Alignment explanation
Indices: 217264--217318 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
217254 TTGGAAGTAT
217264 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
217277 TTATGCTGAGTT-AA
1 TTAAG-T-ATTTCAA
217291 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
217304 TTAAGTATTTGAA
1 TTAAGTATTTCAA
217317 TT
1 TT
217319 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:217566 original size:21 final size:21
Alignment explanation
Indices: 217516--217572 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
217506 TGGAGCGTGG
* *
217516 GGGAATCGATACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
217537 GGGAATCGGTTCCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
217558 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
217573 AAGTGTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:218152 original size:15 final size:17
Alignment explanation
Indices: 218126--218157 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
218116 TCTATGGGAA
218126 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
218142 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
218158 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:221152 original size:14 final size:14
Alignment explanation
Indices: 221133--221162 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
221123 CATTACGAAC
221133 ATATGTATGGATGT
1 ATATGTATGGATGT
*
221147 ATATGTATGTATGT
1 ATATGTATGGATGT
221161 AT
1 AT
221163 GTTTTTGCAG
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:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
ATATGTATGGATGT
Found at i:222629 original size:31 final size:33
Alignment explanation
Indices: 222588--222665 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 33
222578 GAAAGTTTTC
* *
222588 AAAATTTATATTTT-TCTTTTTTAAAAT-TA-T
1 AAAATTTATATTTTATATTTTTAAAAATATATT
222618 AAAATTTTATATTTTATATTTTTAAAAATATATT
1 AAAA-TTTATATTTTATATTTTTAAAAATATATT
*
222652 AAAA-ATATATTTTA
1 AAAATTTATATTTTA
222666 ATATAATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 4 0.10
31 10 0.24
32 20 0.49
33 2 0.05
34 5 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (33 bp):
AAAATTTATATTTTATATTTTTAAAAATATATT
Found at i:225823 original size:7 final size:7
Alignment explanation
Indices: 225811--225846 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
225801 CCCACCCGAC
225811 CCGTTGA
1 CCGTTGA
225818 CCGTTGA
1 CCGTTGA
225825 CCGTTGA
1 CCGTTGA
*
225832 TCGTTGA
1 CCGTTGA
*
225839 CAGTTGA
1 CCGTTGA
225846 C
1 C
225847 TGGGCATTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.31
Consensus pattern (7 bp):
CCGTTGA
Found at i:228593 original size:32 final size:31
Alignment explanation
Indices: 228520--228596 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
228510 CTATTGTAAC
* * *
228520 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCAGCCCTAAGATCAT
** **
228551 TCTCGGGTAGGCCCTGCAGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCAGCCCTAAGAT-CAT
228583 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
228597 CGTGGCCCCG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCAGCCCTAAGATCAT
Found at i:228931 original size:21 final size:21
Alignment explanation
Indices: 228905--228948 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
228895 AATATACGTC
228905 TGAATCAATAAGGAAATTATA
1 TGAATCAATAAGGAAATTATA
228926 TGAATCAATAAGGAAATTATA
1 TGAATCAATAAGGAAATTATA
228947 TG
1 TG
228949 GCTTTCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.30
Consensus pattern (21 bp):
TGAATCAATAAGGAAATTATA
Found at i:234079 original size:15 final size:15
Alignment explanation
Indices: 234018--234089 Score: 55
Period size: 15 Copynumber: 5.1 Consensus size: 15
234008 AAATTCTAAA
234018 TATTTAAAT-AAAAT
1 TATTTAAATAAAAAT
* *
234032 TATTTATATAAAGAT
1 TATTTAAATAAAAAT
* *
234047 TCA-TT-GAT-AATA-
1 T-ATTTAAATAAAAAT
234059 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
234074 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
234089 T
1 T
234090 CATCAATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
11 1 0.02
12 3 0.07
13 5 0.11
14 13 0.29
15 22 0.49
16 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:234082 original size:42 final size:41
Alignment explanation
Indices: 234017--234104 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 41
234007 GAAATTCTAA
* **
234017 ATATTTAAATAAAATTATTTATATAAAGATTCATTGATAAT
1 ATATTTAAATAAAATTATTTATATAAAAATTCATCAATAAT
234058 ATATTTAAATAAAAATTATTTATATAAAAATTCATCAATAAT
1 ATATTTAAAT-AAAATTATTTATATAAAAATTCATCAATAAT
234100 ATATT
1 ATATT
234105 ATTTTATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
41 10 0.23
42 33 0.77
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.43
Consensus pattern (41 bp):
ATATTTAAATAAAATTATTTATATAAAAATTCATCAATAAT
Found at i:240752 original size:54 final size:54
Alignment explanation
Indices: 240692--241307 Score: 840
Period size: 54 Copynumber: 11.4 Consensus size: 54
240682 TCTTTTGCTA
* *
240692 ACGGGTTCGTTTCCC-CTTTCTTTAGGGAGTAGGAACTCGAATAATCTTCTGCCT
1 ACGGGTTCG-CTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* * * * *
240746 ATGGGTTCGCTCCCTCTTTGCTTGAGGTAGT-GGAACTCGAACAATCTTCTACCC
1 ACGGGTTCGCTCCCTCTTT-CTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* * * * *
240800 ATGGGTTCTCTCCCTCTTTCTTTAGGGATTAGGAACTCGAATAATCTTCTGCCA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* * *
240854 ACAGGTTCGCTCCCTCGTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCC
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* * * *
240908 ACGGGTTCGCTCACTCTTTCTTTAGGGAGTAGGAACTCGAACAATTTTCTACCA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* * * *
240962 ACGGGTTCACTCCCTCTTTGTTTTGGGAGTAGGAACTCGAACAATATTCTGCCT
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* * *
241016 ACGAGTTCGCTCCCTCTTTCTTTAGGGGGTAGGAACTCCAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* * *
241070 ACGGGTTAGCTCCCTCTTTCTTTAGGGAGTAGGAACTTGAACAATCTTCTGCCA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* * * * *
241124 ATGGGTTCTCTCACTATTTCTTTAGAGAGTAGGAACTCGAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* * *
241178 ATGGGTTCGCTCTCTCTTTCTTTAGGGAGTAGGAACTTGAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
* *
241232 ACTGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCA
1 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
*
241286 ACGGGTTCGCTCCCTCATTCTT
1 ACGGGTTCGCTCCCTCTTTCTT
241308 ATGAATGCAT
Statistics
Matches: 492, Mismatches: 67, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
53 12 0.02
54 471 0.96
55 9 0.02
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (54 bp):
ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTAGGAACTCGAACAATCTTCTGCCT
Found at i:242456 original size:124 final size:125
Alignment explanation
Indices: 242235--242491 Score: 372
Period size: 124 Copynumber: 2.1 Consensus size: 125
242225 CCTTCACTAG
* * * * *
242235 TGCCCCAACATTATCTTATATTGGTACGGGCCTTCAAAATGCCCCAATACCTCAAATTGTAAGGT
1 TGCCCCAACATTATCTTATACTGGTACAGGCCTTCAAAATACCCCAACACCTCAAATTGTAAGGC
* *
242300 TCATTCTCAATGCATCCTTGGTCCGAATCTTGTCATCTCAACATAATATGGGTTCAGTCA
66 TCATTCTCAATGCATCATTGGTCCGAATCTTGTCATCTCAACATAATATGGGTTCAATCA
*
242360 TGCCCCAACATTATCTTATACTGGTACAGGCC-TCAAAATACCCTAACACCTCAAATTGTAAGGC
1 TGCCCCAACATTATCTTATACTGGTACAGGCCTTCAAAATACCCCAACACCTCAAATTGTAAGGC
* * * * * * *
242424 TCATTCTTAATGCCTCATTGGTCTGCATCTTGTCATCTCAACATGATGTGGTTTCAATCA
66 TCATTCTCAATGCATCATTGGTCCGAATCTTGTCATCTCAACATAATATGGGTTCAATCA
242484 TGCCCCAA
1 TGCCCCAA
242492 TGTGTGTATT
Statistics
Matches: 117, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
124 87 0.74
125 30 0.26
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (125 bp):
TGCCCCAACATTATCTTATACTGGTACAGGCCTTCAAAATACCCCAACACCTCAAATTGTAAGGC
TCATTCTCAATGCATCATTGGTCCGAATCTTGTCATCTCAACATAATATGGGTTCAATCA
Found at i:250264 original size:20 final size:20
Alignment explanation
Indices: 250239--250279 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
250229 ATGGGTCTTG
250239 AATAATTTATTTAATATTTT
1 AATAATTTATTTAATATTTT
*
250259 AATAATTTGTTTAATATTTT
1 AATAATTTATTTAATATTTT
250279 A
1 A
250280 TCCTTAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
AATAATTTATTTAATATTTT
Found at i:256226 original size:23 final size:22
Alignment explanation
Indices: 256199--256241 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
256189 GATACAATTA
256199 TATTAAAATTGATAAAATATAAG
1 TATT-AAATTGATAAAATATAAG
* *
256222 TATTAATTTGTTAAAATATA
1 TATTAAATTGATAAAATATA
256242 TTTATTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
TATTAAATTGATAAAATATAAG
Found at i:258097 original size:6 final size:6
Alignment explanation
Indices: 258079--258123 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
258069 ATGCAATATG
*
258079 AACCCT AAACCCT AACCCT AACCCT AACCCT AATCCT AACCCT AA
1 AACCCT -AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA
258124 TCCTCTACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 30 0.83
7 6 0.17
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (6 bp):
AACCCT
Found at i:258442 original size:45 final size:45
Alignment explanation
Indices: 258388--258476 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
258378 TGGAGTTGTA
258388 TATATTTGAGATAATTATATTTTTTGTTGTTACTTTTGACATATC
1 TATATTTGAGATAATTATATTTTTTGTTGTTACTTTTGACATATC
258433 TATATTTGAGATAATTATATTTTTTGTTGTTACTTTTGACATAT
1 TATATTTGAGATAATTATATTTTTTGTTGTTACTTTTGACATAT
258477 TTGTGTAATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (45 bp):
TATATTTGAGATAATTATATTTTTTGTTGTTACTTTTGACATATC
Found at i:263648 original size:20 final size:22
Alignment explanation
Indices: 263623--263663 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
263613 ACAACTCCAC
263623 CCCACC-T-TCACCCTCCAACT
1 CCCACCTTCTCACCCTCCAACT
263643 CCCACCTTCTCACCCTCCAAC
1 CCCACCTTCTCACCCTCCAAC
263664 CTTCATTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 1 0.05
22 12 0.63
ACGTcount: A:0.20, C:0.61, G:0.00, T:0.20
Consensus pattern (22 bp):
CCCACCTTCTCACCCTCCAACT
Found at i:272702 original size:14 final size:14
Alignment explanation
Indices: 272683--272712 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
272673 TTTAGATTTT
*
272683 TTAAAATTACATTA
1 TTAAAAATACATTA
272697 TTAAAAATACATTA
1 TTAAAAATACATTA
272711 TT
1 TT
272713 GATAATTATA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:272802 original size:7 final size:7
Alignment explanation
Indices: 272790--272826 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
272780 AATTATGTGA
272790 TAGGGTT
1 TAGGGTT
272797 TAGGGTT
1 TAGGGTT
**
272804 TATAGTT
1 TAGGGTT
272811 TAGGGTT
1 TAGGGTT
272818 TAGGGTT
1 TAGGGTT
272825 TA
1 TA
272827 AGTTATACAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
TAGGGTT
Found at i:272814 original size:21 final size:20
Alignment explanation
Indices: 272790--272830 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 20
272780 AATTATGTGA
272790 TAGGGTTTAGGGTTTATAGTT
1 TAGGGTTTAGGGTTTA-AGTT
272811 TAGGGTTTAGGGTTTAAGTT
1 TAGGGTTTAGGGTTTAAGTT
272831 ATACACAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (20 bp):
TAGGGTTTAGGGTTTAAGTT
Found at i:273145 original size:17 final size:17
Alignment explanation
Indices: 273116--273148 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
273106 AATTAAAATT
273116 ACAAGACACAATTGAAA
1 ACAAGACACAATTGAAA
273133 ACAAG-CACAAATTGAA
1 ACAAGACAC-AATTGAA
273149 GGAACACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (17 bp):
ACAAGACACAATTGAAA
Found at i:274110 original size:2 final size:2
Alignment explanation
Indices: 274103--274128 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
274093 TCTTAATTTA
274103 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
274129 GAAGCATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:277350 original size:27 final size:26
Alignment explanation
Indices: 277296--277351 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
277286 ATTGAAGCAT
* *
277296 GGGATGATGGGGAGAGCACAAGCGAA
1 GGGATGATGGAGAGAGCACAAGCAAA
**
277322 GGGAGTGATGGAGAGAGCACCGGCAAA
1 GGGA-TGATGGAGAGAGCACAAGCAAA
277349 GGG
1 GGG
277352 GAGGGGATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.32, C:0.12, G:0.48, T:0.07
Consensus pattern (26 bp):
GGGATGATGGAGAGAGCACAAGCAAA
Found at i:280806 original size:11 final size:12
Alignment explanation
Indices: 280777--280808 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
280767 AAATTAATAT
*
280777 TATTTTTTATAA
1 TATTTTTGATAA
280789 TATTTTTGATAA
1 TATTTTTGATAA
280801 TATTTTTG
1 TATTTTTG
280809 TTAAAACCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (12 bp):
TATTTTTGATAA
Found at i:287064 original size:22 final size:22
Alignment explanation
Indices: 287022--287064 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
287012 CATTTTTAAA
*
287022 TAAATTAAATTTATTATTATTT
1 TAAATTAAATTTATTAATATTT
*
287044 TAAATT-AGTTTATGTAATATT
1 TAAATTAAATTTAT-TAATATT
287065 AAATTCGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (22 bp):
TAAATTAAATTTATTAATATTT
Found at i:288484 original size:18 final size:20
Alignment explanation
Indices: 288445--288484 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
288435 TATATTTTTT
288445 AAATAGTATAATGTGATTATA
1 AAATAGTATAATGT-ATTATA
288466 AAATAGTAT-ATGT-TTATA
1 AAATAGTATAATGTATTATA
288484 A
1 A
288485 TTTTATAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.40
Consensus pattern (20 bp):
AAATAGTATAATGTATTATA
Found at i:290299 original size:3 final size:3
Alignment explanation
Indices: 290291--290349 Score: 77
Period size: 3 Copynumber: 19.7 Consensus size: 3
290281 TTAAATGAAT
*
290291 ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA ATA ATA ATA ATT A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
290336 AT- ATA ATAA ATA AT
1 ATA ATA AT-A ATA AT
290350 TAAAATATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
2 3 0.06
3 41 0.82
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:290355 original size:9 final size:8
Alignment explanation
Indices: 290283--290356 Score: 53
Period size: 9 Copynumber: 8.6 Consensus size: 8
290273 AGTAGAAATT
290283 AAATGAATA
1 AAAT-AATA
*
290292 TAATAATA
1 AAATAATA
290300 ATAATAATA
1 A-AATAATA
290309 ATAATAAT-
1 A-AATAATA
*
290317 TAATAATA
1 AAATAATA
290325 ATAATAATTA
1 A-AATAA-TA
290335 AATATAAT-
1 AA-ATAATA
290343 AAATAATTA
1 AAATAA-TA
290352 AAATA
1 AAATA
290357 TATACATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
7 10 0.19
8 7 0.13
9 30 0.56
10 7 0.13
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (8 bp):
AAATAATA
Found at i:290485 original size:11 final size:11
Alignment explanation
Indices: 290456--290494 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
290446 TGAAATATTA
290456 AATATAATTAAT
1 AATATAA-TAAT
290468 AAT-TAATAAT
1 AATATAATAAT
*
290478 AATATAATTAT
1 AATATAATAAT
290489 AATATA
1 AATATA
290495 TGTTGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 7 0.28
11 15 0.60
12 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATAATAAT
Found at i:301065 original size:2 final size:2
Alignment explanation
Indices: 301058--301094 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
301048 ATTGAAAGCT
301058 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
301095 GGTGGACTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:302260 original size:2 final size:2
Alignment explanation
Indices: 302253--302288 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
302243 TGAACGGATG
302253 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
302289 ATAAAGGAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:305855 original size:19 final size:19
Alignment explanation
Indices: 305833--305904 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
305823 TGAAATACAA
* *
305833 TATGACCTCTGATTTTTGT
1 TATGATCTCTGATTTCTGT
* * * **
305852 TATGAACTTTGATATCCAT
1 TATGATCTCTGATTTCTGT
305871 TATGATCTCTGATTTCTGT
1 TATGATCTCTGATTTCTGT
*
305890 TCTGATCTCTGATTT
1 TATGATCTCTGATTT
305905 ATGATATCTC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (19 bp):
TATGATCTCTGATTTCTGT
Found at i:307738 original size:12 final size:12
Alignment explanation
Indices: 307708--307751 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
307698 CATTTTCCAC
307708 TTTCATATTCAT
1 TTTCATATTCAT
**
307720 TCACATATTCAT
1 TTTCATATTCAT
307732 TTTCATATTCCAT
1 TTTCATATT-CAT
*
307745 GTTCATA
1 TTTCATA
307752 ATAAATAGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.50
Consensus pattern (12 bp):
TTTCATATTCAT
Found at i:307846 original size:19 final size:19
Alignment explanation
Indices: 307794--307850 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
307784 TGAATTAGAA
* *
307794 CTTATTTTCAGACTCATAG
1 CTTATTTTCAAATTCATAG
* * *
307813 CTTACTGTCATATTCATAG
1 CTTATTTTCAAATTCATAG
307832 CTTATTTTCAAATTCATAG
1 CTTATTTTCAAATTCATAG
307851 TCCAATGCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (19 bp):
CTTATTTTCAAATTCATAG
Found at i:313679 original size:13 final size:13
Alignment explanation
Indices: 313661--313685 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
313651 TGTAATTTGA
313661 AATAAATAAAAAG
1 AATAAATAAAAAG
313674 AATAAATAAAAA
1 AATAAATAAAAA
313686 AACTATATAC
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Found at i:316011 original size:51 final size:51
Alignment explanation
Indices: 315890--316257 Score: 384
Period size: 51 Copynumber: 7.0 Consensus size: 51
315880 TCTTTTGCCT
* * * * * *
315890 ACGGGTTCGCTCCCTCTTCCTTCAGGGAGTATAGAACTTTGAAAATCTTCTGCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAAC-TCGAACATC-T-T-CAA
* *
315945 ACGAGTTCTCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
*
315996 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-G
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* * * * * **
316046 ACTGGGTTCGCTCCCTT-TTTCTTCAGGGAGTATAGAATTCAAAAATCTTCTTCTT
1 AC-GGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTC--GAA-CATCTTCAA
* *
316101 ACGGGTTCGCTCCTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAA
1 ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
*
316152 ACGGGTTCGCTCCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-G
1 ACGGGTTCGCT-CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
* *
316203 ACTGGGTTCGCTCCCTTTTTCTCTTTAAAGAGTATA-AGACTCGAACAATCTTCAA
1 AC-GGGTTCGCT-CCTTCTT-TCTTTAAGGAGTATAGA-ACTCGAAC-ATCTTCAA
316258 CAATCGCGTC
Statistics
Matches: 268, Mismatches: 32, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
50 2 0.01
51 98 0.37
52 60 0.22
53 29 0.11
54 46 0.17
55 33 0.12
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (51 bp):
ACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAA
Found at i:316114 original size:105 final size:105
Alignment explanation
Indices: 315888--316257 Score: 378
Period size: 105 Copynumber: 3.5 Consensus size: 105
315878 AATCTTTTGC
* * * * * * *
315888 CTACGGGTTCGCTCCCTCTTCCTTCAGGGAGTATAGAACTTTGAAAATCTTCTGCAAACGAGTTC
1 CTACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAAC-TCGAACATC-T-T-CAAACGGGTTC
* * * *
315953 TCT-CCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-A
62 GCTCCCTTCTTTCTTCAAGGAGTATAGAACTCAAAAATCTTCGA
* *
315995 -AACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTC-GACTGGGTTCGCT
1 CTACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAAC-GGGTTCGCT
* * **
316058 CCCTT-TTTCTTCAGGGAGTATAGAATTCAAAAATCTTCTT
65 CCCTTCTTTCTTCAAGGAGTATAGAACTCAAAAATCTTCGA
* *
316098 CTTACGGGTTCGCTCCTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCT
1 C-TACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
* * *
316163 CCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCGA
65 CCCTTCTTTCTTCAAGGAGTATAGAACTCAAAAATCTTCGA
* *
316204 CT--GGGTTCGCTCCCTTTTTCTCTTTAAAGAGTATA-AGACTCGAACAATCTTCAA
1 CTACGGGTTCGCT-CCTTCTT-TCTTTAAGGAGTATAGA-ACTCGAAC-ATCTTCAA
316258 CAATCGCGTC
Statistics
Matches: 221, Mismatches: 31, Indels: 23
0.80 0.11 0.08
Matches are distributed among these distances:
101 2 0.01
102 36 0.16
103 14 0.06
104 7 0.03
105 90 0.41
106 72 0.33
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (105 bp):
CTACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTC
CCTTCTTTCTTCAAGGAGTATAGAACTCAAAAATCTTCGA
Found at i:316196 original size:157 final size:157
Alignment explanation
Indices: 315892--316224 Score: 551
Period size: 157 Copynumber: 2.1 Consensus size: 157
315882 TTTTGCCTAC
* * ** *
315892 GGGTTCGCTCCCTCTTCCTTCAGGGAGTATAGAACTTTGAAAATCTTCTGCAAACGAGTTCTCTC
1 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTTCAAAAATCTTCTGCAAACGAGTTCGCTC
* *
315957 CTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
66 CTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
316022 GAGTATAGAACTCGAACATCTTCGACT
131 GAGTATAGAACTCGAACATCTTCGACT
* ** *
316049 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAA-TTCAAAAATCTTCTTCTTACGGGTTCGCTC
1 GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTTCAAAAATCTTCTGCAAACGAGTTCGCTC
316113 CTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTTCTTTCTTTAA
66 CTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCT-CCTTCTTTCTTTAA
316178 GGAGTATAGAACTCGAACATCTTCGACT
130 GGAGTATAGAACTCGAACATCTTCGACT
316206 GGGTTCGCTCCCTTTTTCT
1 GGGTTCGCTCCCTTTTTCT
316225 CTTTAAAGAG
Statistics
Matches: 164, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
156 71 0.43
157 93 0.57
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (157 bp):
GGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTTCAAAAATCTTCTGCAAACGAGTTCGCTC
CTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAG
GAGTATAGAACTCGAACATCTTCGACT
Found at i:316255 original size:157 final size:154
Alignment explanation
Indices: 315949--316238 Score: 472
Period size: 156 Copynumber: 1.9 Consensus size: 154
315939 CTGCAAACGA
* * *
315949 GTTCTCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTT
1 GTTCGCTCCTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTT
**
316014 TCTTTAAGGAGTATAGAACTCGAACATCTTCGACTGGGTTCGCTCCCTTTTTCTTCAGGGAGTAT
66 TCTTTAAGGAGTATAGAACTCGAACATCTTCGACTGGGTTCGCTCCCTTTTTCTTCAAAGAGTAT
*
316079 AGAATTCAAAAATCTTCTTCTTACGG
131 AGAACTCAAAAA--TTCTTCTTACGG
316105 GTTCGCTCCTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCCTTCT
1 GTTCGCTCCTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCT-CCTTCT
*
316170 TTCTTTAAGGAGTATAGAACTCGAACATCTTCGACTGGGTTCGCTCCCTTTTTCTCTTTAAAGAG
65 TTCTTTAAGGAGTATAGAACTCGAACATCTTCGACTGGGTTCGCTCCC-TTTT-TCTTCAAAGAG
316235 TATA
128 TATA
316239 AGACTCGAAC
Statistics
Matches: 125, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
156 55 0.44
157 54 0.43
158 4 0.03
159 12 0.10
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (154 bp):
GTTCGCTCCTTCTCTCTTTAAGGAGCATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTT
TCTTTAAGGAGTATAGAACTCGAACATCTTCGACTGGGTTCGCTCCCTTTTTCTTCAAAGAGTAT
AGAACTCAAAAATTCTTCTTACGG
Found at i:316294 original size:55 final size:55
Alignment explanation
Indices: 316231--316428 Score: 351
Period size: 55 Copynumber: 3.6 Consensus size: 55
316221 TTCTCTTTAA
*
316231 AGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAG
1 AGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAG
* *
316286 AGAGTATAAGACTCGAACAATTTTCAATGATCGCGTCTGCCCCCTATTTCTTCAG
1 AGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAG
* *
316341 AGAGTATAAGACTCGAACAATCTTCAACGATCGCATCTGCCCCCTATTTCTTTAG
1 AGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAG
316396 AGAGTATAAGACTCGAACAATCTTCAACGATCG
1 AGAGTATAAGACTCGAACAATCTTCAACGATCG
316429 TTGGGAAACC
Statistics
Matches: 136, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 136 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (55 bp):
AGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAG
Found at i:317447 original size:17 final size:17
Alignment explanation
Indices: 317425--317457 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
317415 ATTTTTTCAT
317425 TTTTTTTTTTCATTTTA
1 TTTTTTTTTTCATTTTA
317442 TTTTTTTTTTCATTTT
1 TTTTTTTTTTCATTTT
317458 TCATTTTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTTCATTTTA
Found at i:317457 original size:7 final size:7
Alignment explanation
Indices: 317417--317464 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
317407 AAACCCTCAT
317417 TTTTTCA
1 TTTTTCA
*
317424 TTTTT-T
1 TTTTTCA
317430 TTTTTCA
1 TTTTTCA
317437 -TTTT-A
1 TTTTTCA
317442 TTTTT--
1 TTTTTCA
317447 TTTTTCA
1 TTTTTCA
317454 TTTTTCA
1 TTTTTCA
317461 TTTT
1 TTTT
317465 CACTCATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
5 6 0.17
6 13 0.37
7 16 0.46
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCA
Found at i:317464 original size:13 final size:13
Alignment explanation
Indices: 317417--317466 Score: 59
Period size: 13 Copynumber: 4.0 Consensus size: 13
317407 AAACCCTCAT
**
317417 TTTTTCATTTTTT
1 TTTTTCATTTTCA
317430 TTTTTCATTTT-A
1 TTTTTCATTTTCA
*
317442 TTTTT-TTTTTCA
1 TTTTTCATTTTCA
317454 TTTTTCATTTTCA
1 TTTTTCATTTTCA
317467 CTCATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 4 0.12
12 11 0.34
13 17 0.53
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:317476 original size:30 final size:30
Alignment explanation
Indices: 317416--317476 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
317406 GAAACCCTCA
** **
317416 TTTTTTCATTTTTTTTTTTCATTTTATTTT
1 TTTTTTCATTTTTCATTTTCATCATATTTT
317446 TTTTTTCATTTTTCATTTTCACTCAT-TTTT
1 TTTTTTCATTTTTCATTTTCA-TCATATTTT
317476 T
1 T
317477 CTTCTTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTTTCATTTTTCATTTTCATCATATTTT
Found at i:320951 original size:8 final size:8
Alignment explanation
Indices: 320938--320965 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
320928 AAAAGAAGAT
320938 ATATATAC
1 ATATATAC
320946 ATATATAC
1 ATATATAC
320954 ATATATAC
1 ATATATAC
320962 ATAT
1 ATAT
320966 GGGAGAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:329132 original size:13 final size:13
Alignment explanation
Indices: 329114--329138 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
329104 TGTAATTTGA
329114 AATAAATAAAAAG
1 AATAAATAAAAAG
329127 AATAAATAAAAA
1 AATAAATAAAAA
329139 AAACTATATA
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Found at i:331965 original size:26 final size:27
Alignment explanation
Indices: 331936--331998 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
331926 TTAAAAAAAT
*
331936 ATTTAATATTTCAAA-TATATTT-GATA
1 ATTTAATATTT-AAAGTATATTTAGAAA
* *
331962 ATTTAAAATTTAAAGTATTTTTAGAAA
1 ATTTAATATTTAAAGTATATTTAGAAA
331989 ATTTTAATAT
1 A-TTTAATAT
331999 GAAAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 3 0.10
26 16 0.53
27 4 0.13
28 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (27 bp):
ATTTAATATTTAAAGTATATTTAGAAA
Found at i:339931 original size:41 final size:41
Alignment explanation
Indices: 339824--339957 Score: 155
Period size: 41 Copynumber: 3.3 Consensus size: 41
339814 GCGCTTATTC
* * *
339824 AAAAATGCCAC--TATATATGAAACCTATTATGGCGATTGTAT
1 AAAAATGCCACGATATATATG--CCCTATTGTGGCGTTTGTAT
* *
339865 AAAAATGCCACGATATATATACCCTATTGTGACGTTTGTAT
1 AAAAATGCCACGATATATATGCCCTATTGTGGCGTTTGTAT
* * *
339906 AAAAATGCCACGATATATATGCCCTATTGCGGCATTTGTTT
1 AAAAATGCCACGATATATATGCCCTATTGTGGCGTTTGTAT
*
339947 AAAAACGCCAC
1 AAAAATGCCAC
339958 TAAAGAATTA
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 73 0.91
43 7 0.09
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.31
Consensus pattern (41 bp):
AAAAATGCCACGATATATATGCCCTATTGTGGCGTTTGTAT
Found at i:341452 original size:22 final size:21
Alignment explanation
Indices: 341416--341468 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
341406 TTATTTTGTA
*
341416 ATTTTTAAAAATTCA-TTACTT
1 ATTTTTAAAAATTCAGTGAC-T
*
341437 ATTTTTAAATAGTTCAGTGACT
1 ATTTTTAAA-AATTCAGTGACT
341459 ATTTTTAAAA
1 ATTTTTAAAA
341469 TTTATCCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.36
22 15 0.54
23 3 0.11
ACGTcount: A:0.38, C:0.08, G:0.06, T:0.49
Consensus pattern (21 bp):
ATTTTTAAAAATTCAGTGACT
Found at i:343670 original size:14 final size:15
Alignment explanation
Indices: 343646--343675 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
343636 CCTCAATCCG
343646 AAGACACCATCCAAC
1 AAGACACCATCCAAC
343661 AAGA-ACCATCCAAC
1 AAGACACCATCCAAC
343675 A
1 A
343676 TTCGAGATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.37, G:0.07, T:0.07
Consensus pattern (15 bp):
AAGACACCATCCAAC
Found at i:350513 original size:22 final size:22
Alignment explanation
Indices: 350470--350526 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
350460 TTACTTTGTC
350470 TAAATAATTAA-TTATTTCAATT
1 TAAAT-ATTAATTTATTTCAATT
350492 TAAATATTAATTTAATTT-AATT
1 TAAATATTAATTT-ATTTCAATT
* *
350514 TATATAATAATTT
1 TAAATATTAATTT
350527 TAAAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.16
22 22 0.71
23 4 0.13
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TAAATATTAATTTATTTCAATT
Found at i:351172 original size:31 final size:31
Alignment explanation
Indices: 351131--351191 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
351121 CAGTTATGTC
* *
351131 AGGGATCATATTGCAAATGGACTAAATGTTT
1 AGGGACCATATTACAAATGGACTAAATGTTT
351162 AGGGACCATATTACAAATGGACTAAATGTT
1 AGGGACCATATTACAAATGGACTAAATGTT
351192 GGGGGATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (31 bp):
AGGGACCATATTACAAATGGACTAAATGTTT
Found at i:351204 original size:31 final size:31
Alignment explanation
Indices: 351131--351204 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
351121 CAGTTATGTC
* *
351131 AGGGATCATATTGCAAATGGACTAAATGTTT
1 AGGGATCATATTACAAATGGACTAAATGTTG
*
351162 AGGGACCATATTACAAATGGACTAAATGTTG
1 AGGGATCATATTACAAATGGACTAAATGTTG
* *
351193 GGGGATTATATT
1 AGGGATCATATT
351205 GCAAGTTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.31
Consensus pattern (31 bp):
AGGGATCATATTACAAATGGACTAAATGTTG
Found at i:351337 original size:2 final size:2
Alignment explanation
Indices: 351330--351363 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
351320 GCATAAATTC
351330 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
351364 CGATCCATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:353575 original size:31 final size:31
Alignment explanation
Indices: 353540--353598 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
353530 TATAATCCCC
353540 CAACATTTAATCCGTTTACAATATGGTCTCT
1 CAACATTTAATCCGTTTACAATATGGTCTCT
* **
353571 CAACATTTAGTCCGTTTGTAATATGGTC
1 CAACATTTAATCCGTTTACAATATGGTC
353599 CCCGATGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (31 bp):
CAACATTTAATCCGTTTACAATATGGTCTCT
Found at i:355864 original size:71 final size:71
Alignment explanation
Indices: 355785--355916 Score: 203
Period size: 71 Copynumber: 1.9 Consensus size: 71
355775 GGATCAAATC
355785 AAAATATAAATAAGAATGAGTCAATTTCATATACAAAT-ATAATTTTAAGGACAAAATTGAAGTA
1 AAAATATAAATAAGAATGAGTCAATTTCATATACAAATGA-AATTTTAAGGACAAAATTGAAGTA
355849 AATTACA
65 AATTACA
* * * * *
355856 AAAATATAAATAAGTATGGGTCAATTTCATATATAGATGAAATTTTAAGGACTAAATTGAA
1 AAAATATAAATAAGAATGAGTCAATTTCATATACAAATGAAATTTTAAGGACAAAATTGAA
355917 CAAAGTAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 54 0.98
72 1 0.02
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.31
Consensus pattern (71 bp):
AAAATATAAATAAGAATGAGTCAATTTCATATACAAATGAAATTTTAAGGACAAAATTGAAGTAA
ATTACA
Found at i:356060 original size:2 final size:2
Alignment explanation
Indices: 356055--356092 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
356045 TATAATTTTA
356055 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
356093 CATTTTTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:356601 original size:2 final size:2
Alignment explanation
Indices: 356594--356659 Score: 57
Period size: 2 Copynumber: 32.5 Consensus size: 2
356584 GTTATTTTCA
* *
356594 AT AT AT AT AT AT AT AT AT AT AA ACT AT AC AT -T AT ACT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT
356635 AGT AT AT AT AT AT AT AT AT AGT AT A
1 A-T AT AT AT AT AT AT AT AT A-T AT A
356660 CATTATACTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
1 3 0.06
2 45 0.85
3 5 0.09
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:356650 original size:38 final size:38
Alignment explanation
Indices: 356599--356683 Score: 143
Period size: 38 Copynumber: 2.2 Consensus size: 38
356589 TTTCAATATA
*
356599 TATATATATATATATAAACTATACATTATACTTATAAG
1 TATATATATATATATAAACTATACATTATACTTATAAC
* *
356637 TATATATATATATATATAGTATACATTATACTTATAAC
1 TATATATATATATATAAACTATACATTATACTTATAAC
356675 TATATATAT
1 TATATATAT
356684 TAGTATACAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (38 bp):
TATATATATATATATAAACTATACATTATACTTATAAC
Found at i:356700 original size:38 final size:38
Alignment explanation
Indices: 356599--356704 Score: 142
Period size: 38 Copynumber: 2.8 Consensus size: 38
356589 TTTCAATATA
* * *
356599 TATATATATATATATAAACTATACATTATACTTATAAG
1 TATATATATATATATACAGTATACATTATACTTATAAC
*
356637 TATATATATATATATATAGTATACATTATACTTATAAC
1 TATATATATATATATACAGTATACATTATACTTATAAC
* *
356675 TATATATAT-TAGTATACATTTTACATTATA
1 TATATATATATA-TATACAGTATACATTATA
356705 AGTATACATT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 2 0.03
38 59 0.97
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (38 bp):
TATATATATATATATACAGTATACATTATACTTATAAC
Found at i:357313 original size:19 final size:19
Alignment explanation
Indices: 357289--357330 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
357279 TATTATAAAT
357289 TCAAAATCTCACAACTTCA
1 TCAAAATCTCACAACTTCA
*
357308 TCAAAATTTCACAACTTCA
1 TCAAAATCTCACAACTTCA
357327 TCAA
1 TCAA
357331 TTGTAACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
TCAAAATCTCACAACTTCA
Found at i:362429 original size:16 final size:16
Alignment explanation
Indices: 362408--362441 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
362398 TTAAAACACA
362408 CTTAAAACACACACTT
1 CTTAAAACACACACTT
362424 CTTAAAACACACACTT
1 CTTAAAACACACACTT
362440 CT
1 CT
362442 CCCCCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.32, G:0.00, T:0.26
Consensus pattern (16 bp):
CTTAAAACACACACTT
Found at i:383702 original size:52 final size:52
Alignment explanation
Indices: 383631--383813 Score: 231
Period size: 52 Copynumber: 3.4 Consensus size: 52
383621 TGAATTAAAT
* * *
383631 AAGTCAAAATAGTATTTAAATCATAGAATTCACAATAATTTATAAGTCAAAC
1 AAGTCAAAACAGTATTTAAATCATAGAAGTCACAACAATTTATAAGTCAAAC
* * *
383683 AAGTCAAAACAGTAATTAAACCATAGAAGTCACAACAATTTATAAATCAAAC
1 AAGTCAAAACAGTATTTAAATCATAGAAGTCACAACAATTTATAAGTCAAAC
* * *
383735 AAAGAAGTCAAAATAATATTTAAATCATAAAAGTCACAACAATTTATAAGTCAAAC
1 ----AAGTCAAAACAGTATTTAAATCATAGAAGTCACAACAATTTATAAGTCAAAC
* *
383791 AAGTCACAACAGTTTTTAAATCA
1 AAGTCAAAACAGTATTTAAATCA
383814 AATACATGCA
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 65 0.59
56 46 0.41
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.26
Consensus pattern (52 bp):
AAGTCAAAACAGTATTTAAATCATAGAAGTCACAACAATTTATAAGTCAAAC
Found at i:383728 original size:26 final size:26
Alignment explanation
Indices: 383655--383815 Score: 76
Period size: 26 Copynumber: 6.0 Consensus size: 26
383645 TTTAAATCAT
* * **
383655 AGAATTCACAATAATTTATAAGTCAA
1 AGAAGTCACAACAATTTATAAACCAA
* * * * *
383681 ACAAGTCAAAAC-AGTAATTAAACCAT
1 AGAAGTCACAACAATTTA-TAAACCAA
383707 AGAAGTCACAACAATTTATAAATCAAACAA
1 AGAAGTCACAACAATTTATAAA-C---CAA
* * *
383737 AGAAGTCAAAATAATATT-TAAATCATA
1 AGAAGTCACAACAAT-TTATAAACCA-A
**
383764 A-AAGTCACAACAATTTATAAGTCAA
1 AGAAGTCACAACAATTTATAAACCAA
* * * *
383789 ACAAGTCACAACAGTTTTTAAATCAA
1 AGAAGTCACAACAATTTATAAACCAA
383815 A
1 A
383816 TACATGCATA
Statistics
Matches: 102, Mismatches: 23, Indels: 20
0.70 0.16 0.14
Matches are distributed among these distances:
25 7 0.07
26 68 0.67
27 6 0.06
30 19 0.19
31 2 0.02
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (26 bp):
AGAAGTCACAACAATTTATAAACCAA
Found at i:386824 original size:24 final size:24
Alignment explanation
Indices: 386797--386844 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
386787 AGTCATTTAG
* *
386797 TCATTAATGGTTTAATGGTTGTTA
1 TCATTAATGGTTTAACGATTGTTA
386821 TCATTAATGGTTTAACGATTGTTA
1 TCATTAATGGTTTAACGATTGTTA
386845 AAGTCTCAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (24 bp):
TCATTAATGGTTTAACGATTGTTA
Found at i:388515 original size:30 final size:30
Alignment explanation
Indices: 388392--388514 Score: 158
Period size: 30 Copynumber: 4.1 Consensus size: 30
388382 TGAAATGACC
* * *
388392 AAAATAGCAAAAATA-AACATTTAAAGGACT
1 AAAATAACAAAAATAGAA-ACTTAAGGGACT
*
388422 AAAATAACAAAAATAGAAACATAAGGGACT
1 AAAATAACAAAAATAGAAACTTAAGGGACT
* *
388452 AAAATAATAAAAATAGAAACTTAAGGGAAT
1 AAAATAACAAAAATAGAAACTTAAGGGACT
* *
388482 AAACTAACAAAAATATAAACTTAAGGGACT
1 AAAATAACAAAAATAGAAACTTAAGGGACT
388512 AAA
1 AAA
388515 CAATAATTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
30 79 0.98
31 2 0.02
ACGTcount: A:0.62, C:0.09, G:0.11, T:0.18
Consensus pattern (30 bp):
AAAATAACAAAAATAGAAACTTAAGGGACT
Found at i:390044 original size:9 final size:9
Alignment explanation
Indices: 390003--390054 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
389993 TATGTAATAG
390003 AATAATTAA
1 AATAATTAA
*
390012 TAATAATATAT
1 -AATAAT-TAA
*
390023 AATAA-TACT
1 AATAATTA-A
390032 AATAATTAA
1 AATAATTAA
390041 AATAATTAA
1 AATAATTAA
390050 AATAA
1 AATAA
390055 AATATAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
8 2 0.05
9 20 0.54
10 13 0.35
11 2 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AATAATTAA
Found at i:390076 original size:34 final size:37
Alignment explanation
Indices: 389998--390076 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 37
389988 AAAAATATGT
* *
389998 AATAGAATAATTAATAATAATATATAATAATACTAATA
1 AATAAAATAATTAATAATAAAATATAATAATAC-AATA
*
390036 ATTAAAATAATTAA-AATAAAATATAA-AATA-AATA
1 AATAAAATAATTAATAATAAAATATAATAATACAATA
390070 AATAAAA
1 AATAAAA
390077 ATACCCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.27
36 4 0.11
37 11 0.30
38 12 0.32
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (37 bp):
AATAAAATAATTAATAATAAAATATAATAATACAATA
Found at i:390079 original size:21 final size:21
Alignment explanation
Indices: 390038--390076 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
390028 TACTAATAAT
*
390038 TAAAATAATTAAAATAAAATA
1 TAAAATAAATAAAATAAAATA
390059 TAAAATAAAT-AAATAAAA
1 TAAAATAAATAAAATAAAA
390077 ATACCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAATAAATAAAATAAAATA
Found at i:390791 original size:66 final size:64
Alignment explanation
Indices: 390709--390926 Score: 202
Period size: 66 Copynumber: 3.4 Consensus size: 64
390699 AAGATATTTT
* *
390709 TTTTGTTTCAAGGGAAACAGTCTCAAAGATATGTGTTTTCAAAAGAAACTGTCTCGAGAGACAAA
1 TTTTGTTTCAAAGGAAACAGACTCAAAGATAT-T-TTTTCAAAAGAAACTGTCTCGAGAGACAAA
390774 A
64 A
* * * * * * *
390775 TTTTGCTTCAAAGGAAACAAACTCAAAGAT-TTTTTCTCAAAATAAATTGTCTCAATAGAGAAAA
1 TTTTGTTTCAAAGGAAACAGACTCAAAGATATTTTT-TCAAAAGAAACTGTCTCGAGAGACAAAA
* * *
390839 TAAATTATTTC-CAGAGAAACAGACTCAAAG--A-TTTTT-AAAAGAAACTGTCTCGAGAGACAA
1 T--TTTGTTTCAAAG-GAAACAGACTCAAAGATATTTTTTCAAAAGAAACTGTCTCGAGAGACAA
390899 AA
63 AA
390901 -TTTGTTTC-AAGAGAAACA-ACTCAAAG
1 TTTTGTTTCAAAG-GAAACAGACTCAAAG
390927 GATACTGATA
Statistics
Matches: 125, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
58 8 0.06
59 15 0.12
62 21 0.17
63 4 0.03
64 29 0.23
65 3 0.02
66 45 0.36
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (64 bp):
TTTTGTTTCAAAGGAAACAGACTCAAAGATATTTTTTCAAAAGAAACTGTCTCGAGAGACAAAA
Found at i:391044 original size:32 final size:32
Alignment explanation
Indices: 391000--391062 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
390990 CATCAGGATA
* *
391000 TTGAATCCCCAAAAATGCTCCAATATTCGATG
1 TTGAATCCCCAAAAATGCCCCAACATTCGATG
* * *
391032 TTGAATCTCCAAAGATTCCCCAACATTCGAT
1 TTGAATCCCCAAAAATGCCCCAACATTCGAT
391063 ATTTCTTCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (32 bp):
TTGAATCCCCAAAAATGCCCCAACATTCGATG
Found at i:392157 original size:29 final size:27
Alignment explanation
Indices: 392110--392196 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 27
392100 CATGTGCTTA
*
392110 TTGTTTTCTTTTTCTTTGCTTTTTCTT
1 TTGTTTTCTTTTTCTTTGCTCTTTCTT
*
392137 TTGTGTTT-TTTTTCTTGTTGCTCTTTGTT
1 TTGT-TTTCTTTTTC-T-TTGCTCTTTCTT
* *
392166 TT-TTTTCTTTGCTTCTTTTCTCTTTGTT
1 TTGTTTTCTTT--TTCTTTGCTCTTTCTT
392194 TTG
1 TTG
392197 ATTGAATCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
27 13 0.26
28 21 0.42
29 13 0.26
30 3 0.06
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.75
Consensus pattern (27 bp):
TTGTTTTCTTTTTCTTTGCTCTTTCTT
Found at i:392177 original size:20 final size:23
Alignment explanation
Indices: 392140--392183 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
392130 TTTTCTTTTG
392140 TGTTTTTTTTCTTGTTGC-TCTT
1 TGTTTTTTTTCTTGTTGCTTCTT
392162 TGTTTTTTTTC-T-TTGCTTCTT
1 TGTTTTTTTTCTTGTTGCTTCTT
392183 T
1 T
392184 TCTCTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.19
21 6 0.29
22 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.75
Consensus pattern (23 bp):
TGTTTTTTTTCTTGTTGCTTCTT
Found at i:392189 original size:15 final size:13
Alignment explanation
Indices: 392118--392195 Score: 56
Period size: 13 Copynumber: 6.2 Consensus size: 13
392108 TATTGTTTTC
*
392118 TTTT-TCTTTGCT
1 TTTTCTCTTTGTT
*
392130 TTTTCT-TTTGTG
1 TTTTCTCTTTGTT
*
392142 TTTT-T-TTTCTT
1 TTTTCTCTTTGTT
* *
392153 GTTGCTCTTTGTT
1 TTTTCTCTTTGTT
*
392166 TTTTTTCTTTGCTT
1 TTTTCTCTTTG-TT
392180 CTTTTCTCTTTGTT
1 -TTTTCTCTTTGTT
392194 TT
1 TT
392196 GATTGAATCT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
11 7 0.14
12 13 0.26
13 16 0.32
14 4 0.08
15 10 0.20
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:394251 original size:14 final size:13
Alignment explanation
Indices: 394207--394249 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
394197 GCTTAAAATG
*
394207 AAATGCATATGCA
1 AAATGCAGATGCA
394220 AAATGCAAAGATG-A
1 AAATGC--AGATGCA
394234 AAATGCAGATGCA
1 AAATGCAGATGCA
394247 AAA
1 AAA
394250 ATATTGATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 5 0.19
13 10 0.38
14 7 0.27
15 4 0.15
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (13 bp):
AAATGCAGATGCA
Found at i:396654 original size:30 final size:30
Alignment explanation
Indices: 396620--396770 Score: 149
Period size: 30 Copynumber: 5.0 Consensus size: 30
396610 TTATAATTAC
* * * *
396620 AAGGACCAGAATGGGAAAAATATAAACTTA
1 AAGGACCAAAATAGCAAAAATAGAAACTTA
* * *
396650 AAGGACCAAAATAGAAAAAATAGACATTTA
1 AAGGACCAAAATAGCAAAAATAGAAACTTA
* *
396680 AAGGACTAAAATAGCAAAAATAGAAACATA
1 AAGGACCAAAATAGCAAAAATAGAAACTTA
* *
396710 AGGGACTAAAATAGCAAAAATAGAAACTTA
1 AAGGACCAAAATAGCAAAAATAGAAACTTA
* ** ** *
396740 AGGGAATAAGCTAGCAAAAATATAAACTTA
1 AAGGACCAAAATAGCAAAAATAGAAACTTA
396770 A
1 A
396771 GTGACTAAAC
Statistics
Matches: 104, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 104 1.00
ACGTcount: A:0.58, C:0.10, G:0.16, T:0.17
Consensus pattern (30 bp):
AAGGACCAAAATAGCAAAAATAGAAACTTA
Found at i:396722 original size:60 final size:60
Alignment explanation
Indices: 396635--396779 Score: 182
Period size: 60 Copynumber: 2.4 Consensus size: 60
396625 CCAGAATGGG
* * * * *
396635 AAAAATATAAACTTAAAGGACCAAAATAGAAAAAATAGACATTTAAAGGACTAAAATAGC
1 AAAAATATAAACTTAAGGGACTAAAATAGAAAAAATAGAAACTTAAAGGAATAAAATAGC
* * * * **
396695 AAAAATAGAAACATAAGGGACTAAAATAGCAAAAATAGAAACTTAAGGGAATAAGCTAGC
1 AAAAATATAAACTTAAGGGACTAAAATAGAAAAAATAGAAACTTAAAGGAATAAAATAGC
*
396755 AAAAATATAAACTTAAGTGACTAAA
1 AAAAATATAAACTTAAGGGACTAAA
396780 CAGTAATTAT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.18
Consensus pattern (60 bp):
AAAAATATAAACTTAAGGGACTAAAATAGAAAAAATAGAAACTTAAAGGAATAAAATAGC
Found at i:404058 original size:43 final size:43
Alignment explanation
Indices: 403992--404097 Score: 178
Period size: 43 Copynumber: 2.5 Consensus size: 43
403982 AGTCCGTAGT
403992 TTTTAGCTCATCAAATAAAGTGGTGATTTATAGCTGTAATAAA
1 TTTTAGCTCATCAAATAAAGTGGTGATTTATAGCTGTAATAAA
* *
404035 TTTTAAG-TCATCAAATAATGTGGTGATTTATAGCTGTGATAAA
1 TTTT-AGCTCATCAAATAAAGTGGTGATTTATAGCTGTAATAAA
404078 TTTTAGCTCATCAAATAAAG
1 TTTTAGCTCATCAAATAAAG
404098 ATGGCTATAT
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
42 2 0.03
43 54 0.93
44 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (43 bp):
TTTTAGCTCATCAAATAAAGTGGTGATTTATAGCTGTAATAAA
Found at i:406447 original size:21 final size:20
Alignment explanation
Indices: 406423--406470 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
406413 AGGTAATAGG
406423 ATTATAAATTATTTCATATTT
1 ATTATAAATTA-TTCATATTT
* *
406444 ATTATCAGATTATTCTTATTT
1 ATTAT-AAATTATTCATATTT
*
406465 AATATA
1 ATTATA
406471 TTAGTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTATAAATTATTCATATTT
Found at i:409232 original size:2 final size:2
Alignment explanation
Indices: 409225--409264 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
409215 TGAGGGGAAA
*
409225 AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
409265 GGTGAGATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:410161 original size:24 final size:25
Alignment explanation
Indices: 410134--410181 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
410124 AATAATAATA
*
410134 ATAATAATAATAATGTAA-ATTAGT
1 ATAATAATAATAATCTAATATTAGT
*
410158 ATAATAATGATAATCTAATATTAG
1 ATAATAATAATAATCTAATATTAG
410182 GACGTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (25 bp):
ATAATAATAATAATCTAATATTAGT
Found at i:410165 original size:3 final size:3
Alignment explanation
Indices: 410119--410147 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
410109 TTTATTAAAT
410119 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
410148 GTAAATTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:410623 original size:137 final size:136
Alignment explanation
Indices: 410329--410623 Score: 330
Period size: 137 Copynumber: 2.2 Consensus size: 136
410319 GCTGTTACTC
* * * *
410329 AGGGAATATCAGAT-TTGAGGA-TGTTGATCCATTCCGCTGCTCTTCAGGGAAAATTGAATCGAG
1 AGGGAATATCAGATCTTGAGGAGAGGTGATCCATTCCACTGCTCTTCAGGGAAAATTGAATCGAA
** * * * * *
410392 GTAAATTTGTTTCACTAGCACTAAGGGAATATCAAATCTTGGAAGGTAGGGATCTGTTCCGCTTC
66 ACAAACTTGTTCCACTAGCACTAAGGGAATATCAAATCTTGGAAAGTAGAGACCTGTTCCGCTTC
410457 TTCTGA
131 TTCTGA
* * * * * *
410463 AGGAAATATCAAATCTGGAAGGAGAGGTGATTCATTCCACTGTTCTTCAGGG-ACATTGAATCGA
1 AGGGAATATCAGATCTTG-AGGAGAGGTGATCCATTCCACTGCTCTTCAGGGAAAATTGAATCGA
* **
410527 AACAGACTTGTTCCACTTTCACTGAAGGGAATATCAAATCTTGGAAAAG-AGAGACCTGTTCCGC
65 AACAAACTTGTTCCACTAGCACT-AAGGGAATATCAAATCTTGG-AAAGTAGAGACCTGTTCCGC
410591 TTAC-TCTGA
128 TT-CTTCTGA
410600 AGGGAATATCAGATCTTAGAGGAG
1 AGGGAATATCAGATCTT-GAGGAG
410624 TTTGATCTAT
Statistics
Matches: 131, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
134 12 0.09
135 2 0.02
136 30 0.23
137 82 0.63
138 5 0.04
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (136 bp):
AGGGAATATCAGATCTTGAGGAGAGGTGATCCATTCCACTGCTCTTCAGGGAAAATTGAATCGAA
ACAAACTTGTTCCACTAGCACTAAGGGAATATCAAATCTTGGAAAGTAGAGACCTGTTCCGCTTC
TTCTGA
Found at i:410723 original size:115 final size:115
Alignment explanation
Indices: 410517--410932 Score: 645
Period size: 115 Copynumber: 3.6 Consensus size: 115
410507 CTTCAGGGAC
* * *
410517 ATTGAATCGAAACAGACTTGTTCCACTTTCACTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
1 ATTGAATCGAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
410582 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTAGAGGAGTTTGATCT
66 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTAGAGGAGTTTGATCT
* * * *
410632 ATTAAATCGAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAACTCTGGGGAAAGAGAGAC
1 ATTGAATCGAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* * *
410697 CTATTCCGCTTACTCTGAAGGGAATATCAGATC-TAAAGGAGTTTGATCC
66 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTAGAGGAGTTTGATCT
* * *
410746 ATTGAATCGGAGCAGACTTGTTCCATTTACTCTGGAGGGAATATCAAATCTTGGAAAAGAGAGAC
1 ATTGAATCGAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
* *
410811 TTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCT
66 CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTAGAGGAGTTTGATCT
** * * *
410861 ATTGAATCGGGGAAGACTTGTTCCATTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGAC
1 ATTGAATCGAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
410926 CTGTTCC
66 CTGTTCC
410933 ACTTGTCTTT
Statistics
Matches: 273, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
114 103 0.38
115 170 0.62
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (115 bp):
ATTGAATCGAAGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAGAGAGAC
CTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTAGAGGAGTTTGATCT
Found at i:410919 original size:229 final size:229
Alignment explanation
Indices: 410516--410932 Score: 692
Period size: 229 Copynumber: 1.8 Consensus size: 229
410506 TCTTCAGGGA
410516 CATTGAATCGAAACAGACTTGTTCCACTTTCACTGAAGGGAATATCAAATCTTGGAAAAGAGAGA
1 CATTGAATCGAAACAGACTTGTTCCACTTTCACTGAAGGGAATATCAAATCTTGGAAAAGAGAGA
*
410581 CCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTAGAGGAGTTTGATCTATTAAATCGAAGCA
66 CCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTAGAGGAGTTTGATCTATTAAATCGAAGAA
*
410646 GACTTGTTCCACTTACTCTGAAGGGAATATCAACTCTGGGGAAAGAGAGACCTATTCCGCTTACT
131 GACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTGGGGAAAGAGAGACCTATTCCGCTTACT
410711 CTGAAGGGAATATCAGATCTAAAGGAGTTTGATC
196 CTGAAGGGAATATCAGATCTAAAGGAGTTTGATC
* * * *
410745 CATTGAATCGGAGCAGACTTGTTCCA-TTTACTCTGGAGGGAATATCAAATCTTGGAAAAGAGAG
1 CATTGAATCGAAACAGACTTGTTCCACTTT-CACTGAAGGGAATATCAAATCTTGGAAAAGAGAG
* * * **
410809 ACTTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCTATTGAATCGGGGA
65 ACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTAGAGGAGTTTGATCTATTAAATCGAAGA
* * *
410874 AGACTTGTTCCATTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCC
130 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTGGGGAAAGAGAGACCTATTCC
410933 ACTTGTCTTT
Statistics
Matches: 173, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
228 3 0.02
229 170 0.98
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (229 bp):
CATTGAATCGAAACAGACTTGTTCCACTTTCACTGAAGGGAATATCAAATCTTGGAAAAGAGAGA
CCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTAGAGGAGTTTGATCTATTAAATCGAAGAA
GACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTGGGGAAAGAGAGACCTATTCCGCTTACT
CTGAAGGGAATATCAGATCTAAAGGAGTTTGATC
Found at i:414760 original size:137 final size:137
Alignment explanation
Indices: 414514--414778 Score: 476
Period size: 137 Copynumber: 1.9 Consensus size: 137
414504 TGACTTTATT
*
414514 TGGGTCTACCTCAATGTCTTTGTTGTTCAACACAAATCCTACGAGTTTCCCAGACATTACCCCGA
1 TGGGTCTACCTCAATGCCTTTGTTGTTCAACACAAATCCTACGAGTTTCCCAGACATTACCCCGA
414579 AGGTACACTTGTTTGGATTAAGCTTTAACTGGGATTTCCTTAATCTTTGGAACAATTTCCTCAGA
66 AGGTACACTTGTTTGGATTAAGCTTTAACTGGGATTTCCTTAATCTTTGGAACAATTTCCTCAGA
414644 TTTTTGA
131 TTTTTGA
* *
414651 TGGGTCTACCTCAATGCCTTTGTTGTTCACCACAAATCCTAGGAGTTTCCCAGACATTACCCCGA
1 TGGGTCTACCTCAATGCCTTTGTTGTTCAACACAAATCCTACGAGTTTCCCAGACATTACCCCGA
* * *
414716 AGGTACACTTGTTTGGATTGAGTTTTAACTGGGATTTCCTTAATCTTTGGAACAGTTTCCTCA
66 AGGTACACTTGTTTGGATTAAGCTTTAACTGGGATTTCCTTAATCTTTGGAACAATTTCCTCA
414779 TATTCTCGAT
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
137 122 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (137 bp):
TGGGTCTACCTCAATGCCTTTGTTGTTCAACACAAATCCTACGAGTTTCCCAGACATTACCCCGA
AGGTACACTTGTTTGGATTAAGCTTTAACTGGGATTTCCTTAATCTTTGGAACAATTTCCTCAGA
TTTTTGA
Found at i:418972 original size:18 final size:18
Alignment explanation
Indices: 418949--418983 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
418939 GTAAATATTT
418949 GTCCCGAAGGACCACTAC
1 GTCCCGAAGGACCACTAC
*
418967 GTCCCGGAGGACCACTA
1 GTCCCGAAGGACCACTA
418984 GATATGTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAC
Found at i:418999 original size:22 final size:21
Alignment explanation
Indices: 418949--419070 Score: 142
Period size: 22 Copynumber: 5.8 Consensus size: 21
418939 GTAAATATTT
418949 GTCCCGAAGGACCAC---TAC
1 GTCCCGAAGGACCACTGATAC
* *
418967 GTCCCGGAGGACCACTAGATAT
1 GTCCCGAAGGACCACT-GATAC
418989 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACT-GATAC
* *
419011 ATCTCGAAGGACCACTGAATAC
1 GTCCCGAAGGACCACTG-ATAC
*
419033 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCACT-GATAC
419055 GTCCCGAAGGACCACT
1 GTCCCGAAGGACCACT
419071 ATAAACCCTC
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
18 14 0.16
21 1 0.01
22 72 0.82
23 1 0.01
ACGTcount: A:0.29, C:0.31, G:0.25, T:0.16
Consensus pattern (21 bp):
GTCCCGAAGGACCACTGATAC
Found at i:419626 original size:20 final size:20
Alignment explanation
Indices: 419603--419660 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
419593 CTAACTGAGA
*
419603 TATAGATACCCTATCTATGG
1 TATAGATACCCTACCTATGG
*
419623 TATAGATACCCTGCCTATGG
1 TATAGATACCCTACCTATGG
*
419643 TATAGATACCCTGCCTAT
1 TATAGATACCCTACCTAT
419661 ATTATGGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (20 bp):
TATAGATACCCTACCTATGG
Found at i:430365 original size:22 final size:21
Alignment explanation
Indices: 430317--430380 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
430307 TTTTGGTGCA
*
430317 GAGGGAATCGATTCCTCCCCCT
1 GAGGGAACCGATTCC-CCCCCT
**
430339 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
430360 GAAGGGGAACCGA-TCCCCCCC
1 G-A-GGGAACCGATTCCCCCCC
430381 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 5 0.14
22 21 0.60
23 9 0.26
ACGTcount: A:0.20, C:0.38, G:0.25, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:430386 original size:21 final size:21
Alignment explanation
Indices: 430362--430401 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
430352 CCCCCTTTGA
*
430362 AGGGGAACCGATCCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
430383 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
430402 TGGGGATCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.42, G:0.25, T:0.07
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:435489 original size:22 final size:22
Alignment explanation
Indices: 435461--435545 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 22
435451 GAAGGACCAC
* *
435461 TACGTCCCGGAGGACCACTGGA
1 TACGTCCCGAAGAACCACTGGA
* *
435483 TACGTCCTGAAGAACCACTAGA
1 TACGTCCCGAAGAACCACTGGA
*
435505 TACGTCCCGAAGTACCACTGGA
1 TACGTCCCGAAGAACCACTGGA
* *
435527 TATGTCTCGAATG-ACCACT
1 TACGTCCCGAA-GAACCACT
435546 ATAAACCCTC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 52 0.98
23 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.20
Consensus pattern (22 bp):
TACGTCCCGAAGAACCACTGGA
Found at i:436152 original size:20 final size:20
Alignment explanation
Indices: 436076--436152 Score: 136
Period size: 20 Copynumber: 3.9 Consensus size: 20
436066 CTAACTGAGA
*
436076 TATAGATACCCTGTCTATGG
1 TATAGATACCCTGCCTATGG
436096 TATAGATACCCTGCCTATGG
1 TATAGATACCCTGCCTATGG
*
436116 TATAGATACCCTTCCTATGG
1 TATAGATACCCTGCCTATGG
436136 TATAGATACCCTGCCTA
1 TATAGATACCCTGCCTA
436153 CATTCTGGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (20 bp):
TATAGATACCCTGCCTATGG
Found at i:436578 original size:26 final size:27
Alignment explanation
Indices: 436549--436600 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
436539 TCAACTTATC
436549 AACTC-TTTTCCATAATTTCATATAAA
1 AACTCATTTTCCATAATTTCATATAAA
** *
436575 AACTCATTTTCTTTAATTTCTTATAA
1 AACTCATTTTCCATAATTTCATATAA
436601 CTTCTTCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (27 bp):
AACTCATTTTCCATAATTTCATATAAA
Found at i:440480 original size:47 final size:48
Alignment explanation
Indices: 440427--440521 Score: 115
Period size: 47 Copynumber: 2.0 Consensus size: 48
440417 TATAGAATAT
* *
440427 CCTAACCTCATG-TCATCTAGTTCACATGC-TTTATTC-AAGAAATTAAA
1 CCTAACCGCATGAT-ATCTAGTTCACATACATTTATTCGAA-AAATTAAA
* *
440474 CCTAACCGCATGATTTCTAGTTTACATACATTTATTCGAAAAATTAAA
1 CCTAACCGCATGATATCTAGTTCACATACATTTATTCGAAAAATTAAA
440522 ATTACACTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
47 23 0.56
48 16 0.39
49 2 0.05
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.35
Consensus pattern (48 bp):
CCTAACCGCATGATATCTAGTTCACATACATTTATTCGAAAAATTAAA
Found at i:441750 original size:4 final size:4
Alignment explanation
Indices: 441741--441766 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
441731 TGCAAAAGTC
441741 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
441767 CATATCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:443627 original size:24 final size:25
Alignment explanation
Indices: 443591--443638 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
443581 AAATATAATA
*
443591 ATAATAATAATAATGTAA-ATTAGT
1 ATAATAATAATAATATAATATTAGT
* *
443615 ATAATAGTGATAATATAATATTAG
1 ATAATAATAATAATATAATATTAG
443639 AACGTCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (25 bp):
ATAATAATAATAATATAATATTAGT
Found at i:446888 original size:22 final size:23
Alignment explanation
Indices: 446860--446904 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
446850 ATAAAATATA
446860 AAAAAATAAAGAAA-TTAAAAAG
1 AAAAAATAAAGAAACTTAAAAAG
*
446882 AAAAAATAAGGAAACTTTAAAAA
1 AAAAAATAAAGAAAC-TTAAAAA
446905 ATTAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.73, C:0.02, G:0.09, T:0.16
Consensus pattern (23 bp):
AAAAAATAAAGAAACTTAAAAAG
Found at i:446934 original size:30 final size:31
Alignment explanation
Indices: 446898--446957 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
446888 TAAGGAAACT
*
446898 TTAAAAAATTAAATTT-ACATAGATTATTTC
1 TTAAAAAACTAAATTTAACATAGATTATTTC
* *
446928 TTAAAAAACTATATTTAACATATATTATTT
1 TTAAAAAACTAAATTTAACATAGATTATTT
446958 GAATATAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (31 bp):
TTAAAAAACTAAATTTAACATAGATTATTTC
Found at i:448839 original size:167 final size:167
Alignment explanation
Indices: 448563--448896 Score: 668
Period size: 167 Copynumber: 2.0 Consensus size: 167
448553 CATCTTACAA
448563 GGGTCATGTAGAAACTGCATATCTTCTGCCTGCATAAGGGTCAGGTATATATAAATGGATCTATG
1 GGGTCATGTAGAAACTGCATATCTTCTGCCTGCATAAGGGTCAGGTATATATAAATGGATCTATG
448628 ATCTTTGTATATTGAGTTAGCGCCTCAAAATATTATTTAAGCAGTAAACGGATATAGCCTGACTA
66 ATCTTTGTATATTGAGTTAGCGCCTCAAAATATTATTTAAGCAGTAAACGGATATAGCCTGACTA
448693 GGAAATACCATACACATTTTCAATATATTGTTCTCCT
131 GGAAATACCATACACATTTTCAATATATTGTTCTCCT
448730 GGGTCATGTAGAAACTGCATATCTTCTGCCTGCATAAGGGTCAGGTATATATAAATGGATCTATG
1 GGGTCATGTAGAAACTGCATATCTTCTGCCTGCATAAGGGTCAGGTATATATAAATGGATCTATG
448795 ATCTTTGTATATTGAGTTAGCGCCTCAAAATATTATTTAAGCAGTAAACGGATATAGCCTGACTA
66 ATCTTTGTATATTGAGTTAGCGCCTCAAAATATTATTTAAGCAGTAAACGGATATAGCCTGACTA
448860 GGAAATACCATACACATTTTCAATATATTGTTCTCCT
131 GGAAATACCATACACATTTTCAATATATTGTTCTCCT
448897 TCTCTAATCT
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 167 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (167 bp):
GGGTCATGTAGAAACTGCATATCTTCTGCCTGCATAAGGGTCAGGTATATATAAATGGATCTATG
ATCTTTGTATATTGAGTTAGCGCCTCAAAATATTATTTAAGCAGTAAACGGATATAGCCTGACTA
GGAAATACCATACACATTTTCAATATATTGTTCTCCT
Found at i:449050 original size:29 final size:29
Alignment explanation
Indices: 449016--449074 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
449006 CCTAAATTAA
449016 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
449045 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
449074 T
1 T
449075 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:453690 original size:29 final size:29
Alignment explanation
Indices: 453656--453715 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
453646 CCTAAATTAA
453656 TTTGATGTCAT-TGCTTACATCAATTTAGT
1 TTTGATGTCATAT-CTTACATCAATTTAGT
453685 TTTGATGTCATATCTTACATCAATTTAGT
1 TTTGATGTCATATCTTACATCAATTTAGT
453714 TT
1 TT
453716 GGTAAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.97
30 1 0.03
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (29 bp):
TTTGATGTCATATCTTACATCAATTTAGT
Found at i:463595 original size:6 final size:6
Alignment explanation
Indices: 463584--463608 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
463574 AAATAAATAA
463584 TTAATT TTAATT TTAATT TTAATT T
1 TTAATT TTAATT TTAATT TTAATT T
463609 AAGTACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:464187 original size:23 final size:23
Alignment explanation
Indices: 464160--464206 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
464150 ATAATTATGA
*
464160 AAAATATATATTAATTTATAAAT
1 AAAATATATATTAATTTAGAAAT
* *
464183 AAAATATTTATTTATTTAGAAAT
1 AAAATATATATTAATTTAGAAAT
464206 A
1 A
464207 TCAGAAAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
AAAATATATATTAATTTAGAAAT
Found at i:464409 original size:20 final size:20
Alignment explanation
Indices: 464374--464413 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
464364 TAAATAAATA
*
464374 TTAAAACATGATTAAAATAAG
1 TTAAAACATAATT-AAATAAG
464395 TTAAAA-ATAATTAAATAAG
1 TTAAAACATAATTAAATAAG
464414 ATTTTAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAAAACATAATTAAATAAG
Found at i:464487 original size:12 final size:12
Alignment explanation
Indices: 464470--464502 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
464460 TTTATGGCTA
464470 AATAATAAT-GAT
1 AATAATAATAG-T
464482 AATAATAATAGT
1 AATAATAATAGT
464494 AATAATAAT
1 AATAATAAT
464503 TAAAAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:465812 original size:3 final size:3
Alignment explanation
Indices: 465804--465892 Score: 135
Period size: 3 Copynumber: 28.7 Consensus size: 3
465794 GGCCTGTTTG
465804 TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
465849 TAA TATA TAA TAA TAAA TAA TAA TAA TAA TAAA TAA TAA TAA TA
1 TAA TA-A TAA TAA T-AA TAA TAA TAA TAA T-AA TAA TAA TAA TA
465893 GAAAATGGAG
Statistics
Matches: 81, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.02
3 67 0.83
4 12 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:465898 original size:16 final size:16
Alignment explanation
Indices: 465805--465892 Score: 141
Period size: 16 Copynumber: 5.8 Consensus size: 16
465795 GCCTGTTTGT
465805 AATAATAATAATAATA
1 AATAATAATAATAATA
465821 AATAA-AATAATAAT-
1 AATAATAATAATAATA
465835 AATAATAATAATAAT-
1 AATAATAATAATAATA
465850 AAT-AT-ATAATAATA
1 AATAATAATAATAATA
465864 AATAATAATAATAATA
1 AATAATAATAATAATA
465880 AATAATAATAATA
1 AATAATAATAATA
465893 GAAAATGGAG
Statistics
Matches: 68, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.12
14 10 0.15
15 23 0.34
16 27 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:466375 original size:110 final size:110
Alignment explanation
Indices: 466237--466979 Score: 1000
Period size: 110 Copynumber: 6.7 Consensus size: 110
466227 TAGAGTCATG
*
466237 AAAAAGGTTGAACAAAATT-TTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
1 AAAAA-GTTGAAC-AAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCA
466301 TTATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
64 TTATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
*
466348 AAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
466413 ATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
66 ATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
*
466458 AAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
466523 ATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
66 ATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
* * *
466568 AAAATGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGAAGAGTTTTTCTC
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT--A-AGTTCTTCTC
* * * *
466630 ATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
63 ATTATGAACT-T-TCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
* * * *
466680 AAAAGGTCGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCAT
* * ** *
466745 TATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGGATTTGAGC
65 TATGAAC-TT-TCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAAAC
* *
466793 AAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTCTC
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT-A--AGTTCTTCTC
* * * *
466855 ATTATGAACTCTACCTGGCAATA-TTGATCTATCAAATGATGAATTCAAAC
63 ATTATGAACT-T-TCTGG-AAAAGTTGATCCATCGAATGATGAATTCAAAC
* * * *
466905 AACAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATAAGTTCTTCTCAT
466970 TATGAACTTT
65 TATGAACTTT
466980 AACTGGCACT
Statistics
Matches: 572, Mismatches: 38, Indels: 44
0.87 0.06 0.07
Matches are distributed among these distances:
107 15 0.03
108 1 0.00
109 15 0.03
110 262 0.46
111 8 0.01
112 137 0.24
113 100 0.17
114 3 0.01
115 12 0.02
116 19 0.03
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (110 bp):
AAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
ATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAAC
Found at i:466856 original size:225 final size:221
Alignment explanation
Indices: 466238--466979 Score: 1136
Period size: 225 Copynumber: 3.3 Consensus size: 221
466228 AGAGTCATGA
*
466238 AAAAGGTTGAACAAAATT-TTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
1 AAAAGGTTGAAC-AAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCAT
466302 TATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCT
65 TATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCT
* *
466367 TCTCATTATGAATTTCTTCTTCCTCTTCAGAT-A-AGTTCTTCTCATTATGAACT-T-TCTGGAA
130 TCTCATTATGAATTTCTTC-T--TCTTCAGATGAGAGTTCTTCTCATTATGAACTCTACCTGGCA
* *
466428 AAGTTGATCCATCGAATGATGAATTCAAAC
192 ATGTTGATCCATCAAATGATGAATTCAAAC
* *
466458 AAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
*
466523 ATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAATGTTGAACAAATTCTT
66 ATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTT
*
466588 CTCATTATGAATTTCTTCTTCTTCAGATGAAGAGTTTTTCTCATTATGAACTCTACCTGGCAATG
131 CTCATTATGAATTTCTTCTTCTTCAGATG-AGAGTTCTTCTCATTATGAACTCTACCTGGCAATG
466653 TTGATCCATCAAATGATGAATTCAAAC
195 TTGATCCATCAAATGATGAATTCAAAC
* * *
466680 AAAAGGTCGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCAT
* * ** * *
466745 TATGAACTTTCTCTGGAAAAGCTGATCCATC-AAGTGATGGATTTGAGCAAAAGGTTGAACAAAT
65 TATGAAC-TT-TCTGGAAAAGTTGATCCATCGAA-TGATGAATTCAAACAAAAAGTTGAACAAAT
466809 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGC
127 TCTTCTCATTATGAATTTCTTCTTCTTCAGATGA-GAGTTCTTCTCATTATGAACTCTACCTGGC
* *
466874 AATATTGATCTATCAAATGATGAATTCAAAC
191 AATGTTGATCCATCAAATGATGAATTCAAAC
* * *
466905 AACAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATAAGTTCTTCTCAT
466970 TATGAACTTT
65 TATGAACTTT
466980 AACTGGCACT
Statistics
Matches: 483, Mismatches: 27, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
217 9 0.02
219 7 0.01
220 157 0.33
221 1 0.00
222 71 0.15
223 29 0.06
224 7 0.01
225 202 0.42
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (221 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATT
ATGAACTTTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTT
CTCATTATGAATTTCTTCTTCTTCAGATGAGAGTTCTTCTCATTATGAACTCTACCTGGCAATGT
TGATCCATCAAATGATGAATTCAAAC
Found at i:467858 original size:114 final size:114
Alignment explanation
Indices: 467695--467918 Score: 342
Period size: 114 Copynumber: 2.0 Consensus size: 114
467685 TATCATGCAG
* * * * * *
467695 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCGATCCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAATCCAGATCAGATAACTCAAAGA
* *
467760 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCAAA
*
467809 TTCATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAAT-CAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACC-AATCCAGATCAGATAACTCAAAG
*
467873 AACACTTCCAGAATATGCTATTGGGCCTCCTTATTTCTACTATGAG
65 AACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAG
467919 AACGTGGAAC
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 97 0.98
115 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAATCCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCAAA
Found at i:468617 original size:12 final size:13
Alignment explanation
Indices: 468600--468666 Score: 93
Period size: 13 Copynumber: 5.1 Consensus size: 13
468590 CCCTTTTTTC
468600 TTTTTTC-TCTTTT
1 TTTTTTCTTC-TTT
468613 TTTTTTCTTCTTCT
1 TTTTTTCTTCTT-T
468627 CTTTTTTCTTC-TT
1 -TTTTTTCTTCTTT
468640 TTTTTTCTTCTTT
1 TTTTTTCTTCTTT
468653 TTTTTTCTTCTTT
1 TTTTTTCTTCTTT
468666 T
1 T
468667 CATTTTTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.20
13 26 0.52
14 4 0.08
15 10 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTCTTCTTT
Found at i:468655 original size:40 final size:41
Alignment explanation
Indices: 468600--468678 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 41
468590 CCCTTTTTTC
468600 TTTTTTCTCTTTTTTTTTTCTTCTTCTC-TTTTTTCTTCTT
1 TTTTTTCTCTTTTTTTTTTCTTCTTCTCATTTTTTCTTCTT
*
468640 TTTTTTCT-TCTTTTTTTTTCTTCTTTTCATTTTTTCTTC
1 TTTTTTCTCT-TTTTTTTTTCTTCTTCTCATTTTTTCTTC
468679 AAGCATAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 1 0.03
40 25 0.69
41 10 0.28
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (41 bp):
TTTTTTCTCTTTTTTTTTTCTTCTTCTCATTTTTTCTTCTT
Found at i:468677 original size:13 final size:13
Alignment explanation
Indices: 468595--468677 Score: 73
Period size: 13 Copynumber: 6.2 Consensus size: 13
468585 TGACCCCCTT
468595 TTTTC-TTTTTTC
1 TTTTCTTTTTTTC
468607 TCTTT-TTTTTTTC
1 T-TTTCTTTTTTTC
468620 TTCTTCTCTTTTTTC
1 TT-TTCT-TTTTTTC
*
468635 TTCTTTTTTTTCTTC
1 TT-TTCTTTTT-TTC
468650 TTTT-TTTTTCTTC
1 TTTTCTTTTT-TTC
*
468663 TTTTCATTTTTTC
1 TTTTCTTTTTTTC
468676 TT
1 TT
468678 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
12 2 0.03
13 31 0.50
14 11 0.18
15 18 0.29
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:480188 original size:12 final size:12
Alignment explanation
Indices: 480171--480203 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
480161 TTTATGGCTA
480171 AATAATAAT-GAT
1 AATAATAATAG-T
480183 AATAATAATAGT
1 AATAATAATAGT
480195 AATAATAAT
1 AATAATAAT
480204 TAAAAGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 19 0.95
13 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (12 bp):
AATAATAATAGT
Done.