Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005833.1 Hibiscus syriacus cultivar Beakdansim tig00013674_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: 149665
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3043 original size:22 final size:21
Alignment explanation
Indices: 3008--3052 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
2998 TCTTCTCATT
*
3008 ACGAACTTCTTCTCACTTATCAA
1 ACGAACTTATTCTCA-TTA-CAA
3031 ACGAA-TTATTCTCATTACAA
1 ACGAACTTATTCTCATTACAA
3051 AC
1 AC
3053 CCTTATACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 8 0.38
23 5 0.24
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (21 bp):
ACGAACTTATTCTCATTACAA
Found at i:3067 original size:117 final size:116
Alignment explanation
Indices: 2801--3415 Score: 476
Period size: 117 Copynumber: 5.3 Consensus size: 116
2791 TTTGGAAGTG
* * * *
2801 TTATTCTCATTATGAA--CTTC-ACTTTGGAAATGTTGATCCACTTCTTTCTGTGATAAATTTGA
1 TTATTCTCATTATGAACCCTTCTAC--TGGAAATATTGATCCACCTCCTTCTGTGATGAA--TGA
* * * * * * ** * * *
2863 GCAAAAAGATTGAACGAGTTCTTTTTATTATG-ATTTTTTCTTTCTTATCGAATGAG
62 G--AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCAAACGAA
* * * * * **
2919 TTTTTATTATTATGAACCCTTCTATTAGAAATGCTGATCCACCTCCTTCTGTGATGAATGAGCAA
1 TTATTCTCATTATGAACCCTTCTACTGGAAATATTGATCCACCTCCTTCTGTGATGAATGAG-AA
* * *
2984 AAGGTTGAATAAGTTCTTCTCATTACGAACTTCTTCTCACTTATCAAACGAA
65 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCAAACGAA
** * * *
3036 TTATTCTCATTACAAACCCTTATACTGGAAAT-TATGATCCATCTTCTTCTGTGATGAATGATGA
1 TTATTCTCATTATGAACCCTTCTACTGGAAATAT-TGATCCACCTCCTTCTGTGATGAATGA-GA
* ** * **
3100 AAAGTTTGAACAAGTTCTTCTTGTTATGAACTTCTTCTTCCTTATTGAAC-AA
64 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCAAACGAA
* * * * * *
3152 GTTCTTCTTATTATGAACTCTTCTACTGGAAATATTGATCCACCTTCTT-TCATGATGAATCA-A
1 -TTATTCTCATTATGAACCCTTCTACTGGAAATATTGATCCACCTCCTTCT-GTGATGAATGAGA
* * * * *
3215 CAATAGGTTGAACAAGTTCTTCTCATCATGAAATT-TTTTCCCTTATCGAACAAA
64 -AA-AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCAAACGAA
* * * ** *
3269 TTATACACATTATGAACCCTTCCACTAAAAATATTGATCCACCTCCTTTTGTGATGAATGAGACA
1 TTATTCTCATTATGAACCCTTCTACTGGAAATATTGATCCACCTCCTTCTGTGATGAATGAGA-A
* * * * *
3334 AAGGTTGAACAAAATT-TTCTCATTATGAATTTCTTATCCCTTATCAAATGAG
65 AAGGTTGAAC-AAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCAAACGAA
* * *
3386 TTCTTCTCATTATGAACCATTCTATTGGAA
1 TTATTCTCATTATGAACCCTTCTACTGGAA
3416 GTTGAATTGT
Statistics
Matches: 394, Mismatches: 87, Indels: 33
0.77 0.17 0.06
Matches are distributed among these distances:
115 1 0.00
116 112 0.28
117 233 0.59
118 15 0.04
119 28 0.07
120 4 0.01
121 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (116 bp):
TTATTCTCATTATGAACCCTTCTACTGGAAATATTGATCCACCTCCTTCTGTGATGAATGAGAAA
AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATCAAACGAA
Found at i:3175 original size:19 final size:20
Alignment explanation
Indices: 3114--3175 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 20
3104 TTTGAACAAG
* *
3114 TTCTTCTTGTTATGAACTTC
1 TTCTTCTTATTATGAACATC
**
3134 TTCTTCCTTA-T-TGAACAAG
1 TTCTT-CTTATTATGAACATC
3153 TTCTTCTTATTATGAAC-TC
1 TTCTTCTTATTATGAACATC
3172 TTCT
1 TTCT
3176 ACTGGAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
18 4 0.12
19 15 0.45
20 11 0.33
21 3 0.09
ACGTcount: A:0.19, C:0.21, G:0.08, T:0.52
Consensus pattern (20 bp):
TTCTTCTTATTATGAACATC
Found at i:3310 original size:116 final size:117
Alignment explanation
Indices: 3161--3378 Score: 291
Period size: 116 Copynumber: 1.9 Consensus size: 117
3151 AGTTCTTCTT
* * ** *
3161 ATTATGAACTCTTCTACTGGAAATATTGATCCACCTTCTTTCATGATGAATCA-ACAATAGGTTG
1 ATTATGAACCCTTCCACTAAAAATATTGATCCACCTCCTTTCATGATGAATCAGACAA-AGGTTG
*
3225 AAC-AAGTTCTTCTCATCATGAAATTT-TT-TCCCTTATCGAACAAATTATACAC
65 AACAAAATT-TTCTCATCATG-AATTTCTTATCCCTTATCGAACAAATTATACAC
** *
3277 ATTATGAACCCTTCCACTAAAAATATTGATCCACCTCCTTTTGTGATGAATGAGACAAAGGTTGA
1 ATTATGAACCCTTCCACTAAAAATATTGATCCACCTCCTTTCATGATGAATCAGACAAAGGTTGA
*
3342 ACAAAATTTTCTCATTATGAATTTCTTATCCCTTATC
66 ACAAAATTTTCTCATCATGAATTTCTTATCCCTTATC
3379 AAATGAGTTC
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
115 5 0.06
116 66 0.75
117 17 0.19
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.36
Consensus pattern (117 bp):
ATTATGAACCCTTCCACTAAAAATATTGATCCACCTCCTTTCATGATGAATCAGACAAAGGTTGA
ACAAAATTTTCTCATCATGAATTTCTTATCCCTTATCGAACAAATTATACAC
Found at i:3392 original size:233 final size:233
Alignment explanation
Indices: 2906--3415 Score: 544
Period size: 233 Copynumber: 2.2 Consensus size: 233
2896 TTTTTTCTTT
* * * * *
2906 CTTATCGAATGAGTTTTTATTATTATGAACCCTTCTATTAGAAATGCTGATCCACCTCCTTCTGT
1 CTTATCGAATGAGTTCTTCTTATTATGAA-CCTTCTATTGGAAATACTGATCCACCTCCTTCTAT
* * * * * *
2971 GATGAATGAGCAAAAGGTTGAATAAGTTCTTCTCATTACGAACTTCTTCTCACTTATCAAACGAA
65 GATGAATCAACAAAAGGTTGAACAAGTTCTTCTCATCACGAAATTCTTCTCACTTATCAAACAAA
* * * ** * *
3036 TTATTCTCATTACAAACCCTTATACTGGAAATTATGATCCATCTTCTTCTGTGATGAATGATGAA
130 TTATACACATTACAAACCCTTACACTAAAAATTATGATCCACCTCCTTCTGTGATGAATGATGAA
* * ** * *
3101 AAGTTTGAACAAGTTCTTCTTGTTATGAACTTCTTCTTC
195 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTATCC
* ** * * *
3140 CTTATTGAACAAGTTCTTCTTATTATGAACTCTTCTACTGGAAATATTGATCCACCTTCTT-TCA
1 CTTATCGAATGAGTTCTTCTTATTATGAAC-CTTCTATTGGAAATACTGATCCACCTCCTTCT-A
* * * * *
3204 TGATGAATCAACAATAGGTTGAACAAGTTCTTCTCATCATGAAATT-TTTTCCCTTATCGAACAA
64 TGATGAATCAACAAAAGGTTGAACAAGTTCTTCTCATCACGAAATTCTTCTCACTTATCAAACAA
** * *
3268 ATTATACACATTATGAACCCTTCCACTAAAAA-TATTGATCCACCTCCTTTTGTGATGAATGA-G
129 ATTATACACATTACAAACCCTTACACTAAAAATTA-TGATCCACCTCCTTCTGTGATGAATGATG
*
3331 ACAAAGGTTGAACAAAATT-TTCTCATTATGAATTTCTTATCC
193 A-AAAGGTTGAAC-AAATTCTTCTCATTATGAACTTCTTATCC
* *
3373 CTTATCAAATGAGTTCTTCTCATTATGAACCATTCTATTGGAA
1 CTTATCGAATGAGTTCTTCTTATTATGAACC-TTCTATTGGAA
3416 GTTGAATTGT
Statistics
Matches: 224, Mismatches: 46, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
232 5 0.02
233 127 0.57
234 92 0.41
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.38
Consensus pattern (233 bp):
CTTATCGAATGAGTTCTTCTTATTATGAACCTTCTATTGGAAATACTGATCCACCTCCTTCTATG
ATGAATCAACAAAAGGTTGAACAAGTTCTTCTCATCACGAAATTCTTCTCACTTATCAAACAAAT
TATACACATTACAAACCCTTACACTAAAAATTATGATCCACCTCCTTCTGTGATGAATGATGAAA
AGGTTGAACAAATTCTTCTCATTATGAACTTCTTATCC
Found at i:10481 original size:15 final size:15
Alignment explanation
Indices: 10461--10493 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10451 AGATATTAAA
10461 GAGGAATTTCTTGAT
1 GAGGAATTTCTTGAT
10476 GAGGAATTTCTTGAT
1 GAGGAATTTCTTGAT
10491 GAG
1 GAG
10494 AAACTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.30, T:0.36
Consensus pattern (15 bp):
GAGGAATTTCTTGAT
Found at i:19776 original size:19 final size:19
Alignment explanation
Indices: 19752--19788 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19742 TCACCATGAG
19752 TACTCCTATAAAAGGTATA
1 TACTCCTATAAAAGGTATA
* *
19771 TACTCCTCTAAAGGGTAT
1 TACTCCTATAAAAGGTAT
19789 CTAACCTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (19 bp):
TACTCCTATAAAAGGTATA
Found at i:22087 original size:6 final size:6
Alignment explanation
Indices: 22065--22184 Score: 100
Period size: 6 Copynumber: 18.7 Consensus size: 6
22055 TCTTTGACCC
* *
22065 CTTTTT GTTTATT CTTTTT CTTTTT CCTTTTTTT CCTTTT CTTTTT CTTTTT
1 CTTTTT CTTT-TT CTTTTT CTTTTT -C--TTTTT CTTTTT CTTTTT CTTTTT
*
22117 CTTTTT CTTTTT -TTTCT CTTTTCT CTTTTCT CTTTTCT CTTTTTT CCTTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTT-T CTTTT-T CTTTT-T C-TTTTT -C-TTTTT
*
22170 CCTTTT -TTTTT CTTT
1 CTTTTT CTTTTT CTTT
22185 CTAACTTTTT
Statistics
Matches: 97, Mismatches: 8, Indels: 18
0.79 0.07 0.15
Matches are distributed among these distances:
5 8 0.08
6 48 0.49
7 24 0.25
8 12 0.12
9 5 0.05
ACGTcount: A:0.01, C:0.20, G:0.01, T:0.78
Consensus pattern (6 bp):
CTTTTT
Found at i:22103 original size:16 final size:14
Alignment explanation
Indices: 22076--22216 Score: 85
Period size: 16 Copynumber: 9.5 Consensus size: 14
22066 TTTTTGTTTA
22076 TTCTTTTTC-TTTT
1 TTCTTTTTCTTTTT
* *
22089 TCCTTTTT-TTCCTT
1 TTCTTTTTCTT-TTT
22103 TTCTTTTTC--TTT
1 TTCTTTTTCTTTTT
22115 TTCTTTTTCTTTTTT
1 TTCTTTTTC-TTTTT
22130 TTCTCTTTTCTCTTTT
1 TTCT-TTTTCT-TTTT
*
22146 CTCTTTTCTCTTTTT
1 TTCTTTT-TCTTTTT
*
22161 TCCTTTTTTCCTTTTT
1 TTC-TTTTT-CTTTTT
22177 TT-TTCTTTCTAACTTTT
1 TTCTT-TTTCT---TTTT
*
22194 TTCTTTTTATTTATTT
1 TTCTTTTT-CTT-TTT
22210 TTCTTTT
1 TTCTTTT
22217 CTTCAAGTGT
Statistics
Matches: 101, Mismatches: 9, Indels: 33
0.71 0.06 0.23
Matches are distributed among these distances:
12 11 0.11
13 8 0.08
14 13 0.13
15 21 0.21
16 36 0.36
17 9 0.09
18 3 0.03
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (14 bp):
TTCTTTTTCTTTTT
Found at i:22201 original size:7 final size:7
Alignment explanation
Indices: 22066--22216 Score: 85
Period size: 7 Copynumber: 20.4 Consensus size: 7
22056 CTTTGACCCC
*
22066 TTTTTGT
1 TTTTTCT
*
22073 TTATTC-
1 TTTTTCT
22079 TTTTTCT
1 TTTTTCT
*
22086 TTTTCCT
1 TTTTTCT
22093 TTTTT-T
1 TTTTTCT
*
22099 CCTTTTC-
1 -TTTTTCT
22106 TTTTTC-
1 TTTTTCT
22112 TTTTTCT
1 TTTTTCT
*
22119 TTTTCTTT
1 TTTT-TCT
22127 TTTTTCT
1 TTTTTCT
22134 CTTTTCTCT
1 -TTTT-TCT
*
22143 TTTCTCT
1 TTTTTCT
*
22150 TTTCTCT
1 TTTTTCT
22157 TTTTTCCT
1 TTTTT-CT
22165 TTTTTCCT
1 TTTTT-CT
*
22173 TTTTTTT
1 TTTTTCT
22180 TCTTTCTAACT
1 T-TTT-T--CT
22191 TTTTTCT
1 TTTTTCT
*
22198 TTTTATTT
1 TTTT-TCT
22206 ATTTTTCT
1 -TTTTTCT
22214 TTT
1 TTT
22217 CTTCAAGTGT
Statistics
Matches: 115, Mismatches: 15, Indels: 28
0.73 0.09 0.18
Matches are distributed among these distances:
6 17 0.15
7 49 0.43
8 35 0.30
9 9 0.08
10 3 0.03
11 2 0.02
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (7 bp):
TTTTTCT
Found at i:30169 original size:53 final size:53
Alignment explanation
Indices: 30103--30434 Score: 475
Period size: 53 Copynumber: 6.2 Consensus size: 53
30093 GAACTCGAAT
* * *
30103 AATCTTTAACAATCGTGTCTACCCCCTATTTCTTCAGAGAGTATAAGACCAAC
1 AATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCAAC
* * * *
30156 AATCTTCATCAATCGCGTTTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-AAC
* * *
30211 AATCTTCAACGATCCTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCAC
1 AATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCAAC
*
30264 AATCTTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C-AAC
* * * *
30319 AATCTTCAACGATCGTGTATGTCCCCTATATCTTCAGAGAGTATAAGACCCAC
1 AATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCAAC
* *
30372 AATCTTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCAC
1 AATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCAAC
30425 AATCTTCAAC
1 AATCTTCAAC
30435 AAATGGGTTC
Statistics
Matches: 250, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
53 153 0.61
54 4 0.02
55 93 0.37
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.30
Consensus pattern (53 bp):
AATCTTCAACGATCGTGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCAAC
Found at i:30215 original size:108 final size:108
Alignment explanation
Indices: 30095--30436 Score: 526
Period size: 108 Copynumber: 3.2 Consensus size: 108
30085 GGAGTATGGA
* * * * *
30095 ACTCGAATAATCTTTAACAATCGTGTCTACCCCCTATTTCTTCAGAGAGTATAAGACCAACAATC
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
* * * * *
30160 TTCATCAATCGCGTTTGCCCCCTATTTCTTCAGAGAGTATAAG
66 TTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* *
30203 ACTCGAACAATCTTCAACGATCCTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
30268 TTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
66 TTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* * *
30311 ACTCGAACAATCTTCAACGATCGTGTATGTCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
1 ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
30376 TTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
66 TTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
*
30419 AC-C-CACAATCTTCAACAA
1 ACTCGAACAATCTTCAACAA
30437 ATGGGTTCGC
Statistics
Matches: 217, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
106 13 0.06
107 1 0.00
108 203 0.94
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (108 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCCCCCTATATCTTCAGAGAGTATAAGACCCACAATC
TTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
Found at i:30451 original size:161 final size:161
Alignment explanation
Indices: 30103--30457 Score: 511
Period size: 161 Copynumber: 2.2 Consensus size: 161
30093 GAACTCGAAT
* * * *
30103 AATCTTTAACAATCGTGTCTACCCCCTATTTCTTCAGAGAGTATAAGACCAACAATCTTCATCAA
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCAACAATCTTCAACAA
* *
30168 TCGCGTTTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCCTGTCTGC
66 TCGCGTATGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCCTGTCTGC
30233 CCCCTATATCTTCAGAGAGTATAAGACCCAC
131 CCCCTATATCTTCAGAGAGTATAAGACCCAC
*
30264 AATCTTCAACGATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-C-AACAATCTTCAAC
* * * * *
30329 GATCGTGTATGTCCCCTATATCTTCAGAGAGTATAAGAC-C-CACAATCTTCAACGATCGTGTCT
64 AATCGCGTATGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCCTGTCT
* *
30392 GCTCCCTATTTCTTCAGAGAGTATAAGACCCAC
129 GCCCCCTATATCTTCAGAGAGTATAAGACCCAC
*
30425 AATCTTCAACAAAT-GGGT-TCGCTCCCTATTTCT
1 AATCTTCAAC-AATCGTGTCT-GCTCCCTATTTCT
30458 CTAGGGAGTA
Statistics
Matches: 174, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
160 1 0.01
161 123 0.71
162 4 0.02
163 46 0.26
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (161 bp):
AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCAACAATCTTCAACAA
TCGCGTATGCCCCCTATATCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCCTGTCTGC
CCCCTATATCTTCAGAGAGTATAAGACCCAC
Found at i:30563 original size:53 final size:53
Alignment explanation
Indices: 30434--30746 Score: 379
Period size: 53 Copynumber: 5.9 Consensus size: 53
30424 CAATCTTCAA
* * * * *
30434 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATGGAACTC-AGACATATTCTT
1 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGA-ACAT-CTCTT
* *
30488 CAAACGGGTTCGCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTCTT
1 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT
* *
30541 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACA--TCTT
1 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT
* * * *
30592 CAAACGAGTTCGCT-CCTACTTTCTTTAAGGAGTATAGAACTCGCACA-ATCTT
1 CAAACGGGTTCGCTCCCT-CTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT
*
30644 CAAACGGGTTCGCTCCCTC--TCTTTAGGGAGTATAGAACTCGAACAATCTTCTG
1 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAC-ATC-TCTT
* * *
30697 AAAACGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCT
1 CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCT
30747 TCTTTTGCTT
Statistics
Matches: 230, Mismatches: 20, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
50 25 0.11
51 46 0.20
52 18 0.08
53 72 0.31
54 45 0.20
55 24 0.10
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (53 bp):
CAAACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT
Found at i:30630 original size:104 final size:102
Alignment explanation
Indices: 30434--30746 Score: 369
Period size: 104 Copynumber: 3.0 Consensus size: 102
30424 CAATCTTCAA
* * * * *
30434 CAAATGGGTTCGCTCCCTATTTCTCTAGGGAGTATGGAACTCAGACATATTCTTCAAACGGGTTC
1 CAAACGGGTTCGCT-CCTCTTTCTTTAGGGAGTATAGAACTC-GA-ACA-TCTTCAAACGGGTTC
* *
30499 GCTCCCCCTTTCTCTAGGGAGTATAGAACTCGAACATCTCTT
62 GCT-CCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT
* *
30541 CAAACGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCGAACATCTTCAAACGAGTTCGCT
1 CAAACGGGTTCGCTCC-TCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCT
* * *
30606 CCTACTTTCTTTAAGGAGTATAGAACTCGCACA-ATCTT
65 CCT-CTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT
*
30644 CAAACGGGTTCGCTCC-CTCTCTTTAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTC
1 CAAACGGGTTCGCTCCTCTTTCTTTAGGGAGTATAGAACTCGAAC-ATCTTC---AAACGGGTTC
* *
30708 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGAAAATCT
62 GCT-CCTCTTTCTTTAGGGAGTATAGAACTCGAACATCT
30747 TCTTTTGCTT
Statistics
Matches: 178, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
101 26 0.15
102 6 0.03
103 22 0.12
104 43 0.24
105 39 0.22
106 8 0.04
107 34 0.19
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (102 bp):
CAAACGGGTTCGCTCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTC
CTCTTTCTTTAGGGAGTATAGAACTCGAACATCTCTT
Found at i:30702 original size:156 final size:157
Alignment explanation
Indices: 30441--30748 Score: 437
Period size: 156 Copynumber: 2.0 Consensus size: 157
30431 CAACAAATGG
* *
30441 GTTCGCTCCCTATTTCTCTAGGGAGTATGGAACTCAGACATATTCTTCAAACGGGTTCGCTCCCC
1 GTTCGCTCCCTATTTCTCTAAGGAGTATAGAACTCAGACATATTCTTCAAACGGGTTCGCT-CCC
* ** * *
30506 CTTTCTCTAGGGAGTATAGAACTCGAACATCTCTTCAAACGGGTTCGCTCCTTCTTTCTTTAAGG
65 CTCTCTCTAGGGAGTATAGAACTCGAACATCTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAAGG
*
30571 AGTATAGAACTCGAACATCTTCAAACGA
130 AGTATAGAACTCGAAAATCTTCAAACGA
*
30599 GTTCGCT-CCTACTTTCTTTAAGGAGTATAGAACTC-GCACA-A-TCTTCAAACGGGTTCGCT-C
1 GTTCGCTCCCTA-TTTCTCTAAGGAGTATAGAACTCAG-ACATATTCTTCAAACGGGTTCGCTCC
*
30659 CCTCTCTTTAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCA
64 CCTCTCTCTAGGGAGTATAGAACTCGAAC-ATC-TCTGAAAACGGGTTCGCTCCCTCTTTCTTCA
*
30724 GGGAGTATAGAACTCGAAAATCTTC
127 AGGAGTATAGAACTCGAAAATCTTC
30749 TTTTGCTTCA
Statistics
Matches: 135, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
154 28 0.21
155 3 0.02
156 68 0.50
157 6 0.04
158 30 0.22
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (157 bp):
GTTCGCTCCCTATTTCTCTAAGGAGTATAGAACTCAGACATATTCTTCAAACGGGTTCGCTCCCC
TCTCTCTAGGGAGTATAGAACTCGAACATCTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAAGGA
GTATAGAACTCGAAAATCTTCAAACGA
Found at i:32171 original size:124 final size:125
Alignment explanation
Indices: 31896--32199 Score: 475
Period size: 124 Copynumber: 2.4 Consensus size: 125
31886 TCAATAATTT
* ** *
31896 CTTGGTCTGAATCTTTTCATCTCAACATGACGTGGGTTTGGTCGCGCCCCAACATTATCTTACAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTACAC
** * * *
31961 TGGTACGGGCCTTCAAAATGCCCCATCACTTCAAATTGTAAGGCTCATTCTTCATGCCTC
66 TGGTACGGGCAATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
* *
32021 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCATGCCCCAACATTATCTTATAC
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTACAC
32086 TGGTACGGG-AATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
66 TGGTACGGGCAATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
* * *
32145 CTTGGTCTGAATCTTGTCTTCTCAACATGATGTGGGTTCATTCGTGCCCCAACAT
1 CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACAT
32200 ATCACAACTT
Statistics
Matches: 164, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
124 96 0.59
125 68 0.41
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (125 bp):
CTTGGTCTGAATCTTTTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTACAC
TGGTACGGGCAATCAAAATGCCCCAACACCTCAAATTGTAAGGCTCATTCTTAATGCCTC
Found at i:33475 original size:16 final size:16
Alignment explanation
Indices: 33457--33486 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33447 TTCATTCTTT
33457 TTTTC-ATTTTTCTCA
1 TTTTCAATTTTTCTCA
33472 TTTTCAATTTTTCTC
1 TTTTCAATTTTTCTC
33487 TTTCTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTCAATTTTTCTCA
Found at i:33510 original size:22 final size:22
Alignment explanation
Indices: 33485--33569 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 22
33475 TCAATTTTTC
*
33485 TCTTTCTTTTCCTTTTTTATTT
1 TCTTTCTTTTTCTTTTTTATTT
*
33507 TCTTT-TTCATTTCTTTTTT-TTA
1 TCTTTCTT--TTTCTTTTTTATTT
*
33529 TCTTTTCTTTTTCTCTTTCTATATT
1 TC-TTTCTTTTTCT-TTTTTAT-TT
*
33554 TCTCTTCTTTCTCTTT
1 TCT-TTCTTTTTCTTT
33570 ATGATGTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
21 2 0.04
22 14 0.28
23 16 0.32
24 6 0.12
25 12 0.24
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (22 bp):
TCTTTCTTTTTCTTTTTTATTT
Found at i:33542 original size:6 final size:6
Alignment explanation
Indices: 33456--33548 Score: 59
Period size: 6 Copynumber: 15.2 Consensus size: 6
33446 TTTCATTCTT
* *
33456 TTTTTC ATTTTTC TCATTTTC AATTTTTC TCTTTC TTTTCC TTTTT- TATTTTC
1 TTTTTC -TTTTTC T--TTTTC --TTTTTC TTTTTC TTTTTC TTTTTC T-TTTTC
* * *
33509 TTTTTC -ATTTC TTTTT- TTTATC -TTTTC TTTTTC TCTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC T
33549 ATATTTCTCT
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
5 13 0.19
6 37 0.54
7 7 0.10
8 10 0.15
10 1 0.01
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:36180 original size:21 final size:21
Alignment explanation
Indices: 36132--36289 Score: 144
Period size: 21 Copynumber: 7.6 Consensus size: 21
36122 CATGTGATGT
* * *
36132 GGTCTTCTCATCTTTACG-AA
1 GGTCTTCTCGTCTTGATGAAA
36152 GGTCTTCTCGTCGTT-ATGAAA
1 GGTCTTCTCGTC-TTGATGAAA
* *
36173 GGTATTCTCGTCTTGATGAAT
1 GGTCTTCTCGTCTTGATGAAA
*
36194 GGTCTTCTCGTCTTGATGAAT
1 GGTCTTCTCGTCTTGATGAAA
* * *
36215 GGCCTTCTCATCTTGATGAAT
1 GGTCTTCTCGTCTTGATGAAA
36236 GG-CATTCTCGTCTTGATG-AA
1 GGTC-TTCTCGTCTTGATGAAA
* * *
36256 TGACATTCTCGTCTTGATGAAT
1 GGTC-TTCTCGTCTTGATGAAA
*
36278 GCTCTTCTCGTC
1 GGTCTTCTCGTC
36290 CTTGGTACAA
Statistics
Matches: 118, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
20 18 0.15
21 98 0.83
22 2 0.02
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.40
Consensus pattern (21 bp):
GGTCTTCTCGTCTTGATGAAA
Found at i:36199 original size:42 final size:42
Alignment explanation
Indices: 36152--36289 Score: 190
Period size: 42 Copynumber: 3.3 Consensus size: 42
36142 TCTTTACGAA
* *
36152 GGTCTTCTCGTCGTT-ATGAAAGGTATTCTCGTCTTGATGAAT
1 GGTCTTCTCGTC-TTGATGAATGGCATTCTCGTCTTGATGAAT
* *
36194 GGTCTTCTCGTCTTGATGAATGGCCTTCTCATCTTGATGAAT
1 GGTCTTCTCGTCTTGATGAATGGCATTCTCGTCTTGATGAAT
*
36236 GG-CATTCTCGTCTTGATGAATGACATTCTCGTCTTGATGAAT
1 GGTC-TTCTCGTCTTGATGAATGGCATTCTCGTCTTGATGAAT
*
36278 GCTCTTCTCGTC
1 GGTCTTCTCGTC
36290 CTTGGTACAA
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
41 3 0.04
42 81 0.95
43 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (42 bp):
GGTCTTCTCGTCTTGATGAATGGCATTCTCGTCTTGATGAAT
Found at i:36234 original size:63 final size:63
Alignment explanation
Indices: 36131--36286 Score: 185
Period size: 63 Copynumber: 2.5 Consensus size: 63
36121 CCATGTGATG
* * * * * *
36131 TGGTCTTCTCATCTTTACGAA-GGTCTTCTCGTCGTTATGAAAGGTATTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAATGGCCTTCTCATCGTTATGAAAGGCATTCTCGTCTTGATGAA
*
36193 TGGTCTTCTCGTCTTGATGAATGGCCTTCTCATC-TTGATGAATGGCATTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAATGGCCTTCTCATCGTT-ATGAAAGGCATTCTCGTCTTGATGAA
*
36256 T-GACATTCTCGTCTTGATGAAT-GCTCTTCTC
1 TGGTC-TTCTCGTCTTGATGAATGGC-CTTCTC
36287 GTCCTTGGTA
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
62 24 0.29
63 58 0.71
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (63 bp):
TGGTCTTCTCGTCTTGATGAATGGCCTTCTCATCGTTATGAAAGGCATTCTCGTCTTGATGAA
Found at i:38725 original size:17 final size:19
Alignment explanation
Indices: 38692--38727 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
38682 TCATCAATCA
38692 ACACCTTCGGCTGGCCATC
1 ACACCTTCGGCTGGCCATC
38711 ACACCTT-GG-TGGCCATC
1 ACACCTTCGGCTGGCCATC
38728 TTCACCCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 2 0.12
19 7 0.41
ACGTcount: A:0.17, C:0.39, G:0.22, T:0.22
Consensus pattern (19 bp):
ACACCTTCGGCTGGCCATC
Found at i:41676 original size:3 final size:3
Alignment explanation
Indices: 41670--41742 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
41660 TATTATTTAT
*
41670 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
41717 -AA AAA TAA AAA T-A TAAA TAA AAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA
41743 AAACAAATGG
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
2 6 0.10
3 51 0.86
4 2 0.03
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:41735 original size:26 final size:27
Alignment explanation
Indices: 41671--41745 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 27
41661 ATTATTTATT
* *
41671 AATAATAATAATAATATAATAATAATAAT
1 AATACTAATAATAATA-AA-AATAATAAA
41700 AATACTAATAATAATAAAAA-AATAAA
1 AATACTAATAATAATAAAAATAATAAA
*
41726 AATA-TAAATAAAAATAAAAA
1 AATACT-AATAATAATAAAAA
41746 CAAATGGACA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.02
26 22 0.52
27 2 0.05
28 2 0.05
29 15 0.36
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (27 bp):
AATACTAATAATAATAAAAATAATAAA
Found at i:48291 original size:8 final size:8
Alignment explanation
Indices: 48278--48341 Score: 128
Period size: 8 Copynumber: 8.0 Consensus size: 8
48268 CTACGAAAAT
48278 GATTATTC
1 GATTATTC
48286 GATTATTC
1 GATTATTC
48294 GATTATTC
1 GATTATTC
48302 GATTATTC
1 GATTATTC
48310 GATTATTC
1 GATTATTC
48318 GATTATTC
1 GATTATTC
48326 GATTATTC
1 GATTATTC
48334 GATTATTC
1 GATTATTC
48342 ATACGTTTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 56 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (8 bp):
GATTATTC
Found at i:50241 original size:60 final size:60
Alignment explanation
Indices: 50142--50269 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 60
50132 TAAAACACAC
* * * * *
50142 AAATGGTCCCTCAACTATATGATGTTGCATTTTTGAGTCCCTTGACTATTAAATGTTACA
1 AAATGGTCCCCCAACTATAGGATGTTGCATTTTTCAGTCCCTCGACTATTAAAAGTTACA
* *
50202 AAATGGTCCCCCAATTATAGGATGTTTC-TTTGTTCAGTCCCTCGACTATTAAAAGTTACA
1 AAATGGTCCCCCAACTATAGGATGTTGCATTT-TTCAGTCCCTCGACTATTAAAAGTTACA
50262 AAATGGTC
1 AAATGGTC
50270 ATCCGACTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 3 0.05
60 57 0.95
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (60 bp):
AAATGGTCCCCCAACTATAGGATGTTGCATTTTTCAGTCCCTCGACTATTAAAAGTTACA
Found at i:54324 original size:51 final size:51
Alignment explanation
Indices: 54181--54401 Score: 212
Period size: 51 Copynumber: 4.2 Consensus size: 51
54171 GGGTGTTGCA
* *
54181 ACTAGTGTAAGTCTGTGATGAGATTAATTTTGGAATTATATGTTAAATTTG
1 ACTAGTGTAAGTCTGTAATGAGATTAATTCTGGAATTATATGTTAAATTTG
* * * * *
54232 ACTAG-G-ATAGTCAGTGATGAGTTTAGTGCTGGAATTATATGTTAAATTTG
1 ACTAGTGTA-AGTCTGTAATGAGATTAATTCTGGAATTATATGTTAAATTTG
* **
54282 ACTAGTGTAAGTTTGTAATGAGATTAATTCTGGAATTATATGTTACGTTTG
1 ACTAGTGTAAGTCTGTAATGAGATTAATTCTGGAATTATATGTTAAATTTG
* * * * *
54333 ACTGGGGTAAGTCAGTGATAAGTGATAAGTTTAGTTCTGGAATTATATGTTAAATTTA
1 ACTAGTGTAAGTC--TG-TAA-TG---AGATTAATTCTGGAATTATATGTTAAATTTG
*
54391 ACTGGTGTAAG
1 ACTAGTGTAAG
54402 ATAGTGATAA
Statistics
Matches: 138, Mismatches: 22, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
49 1 0.01
50 43 0.31
51 50 0.36
52 1 0.01
53 2 0.01
54 3 0.02
55 2 0.01
58 36 0.26
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (51 bp):
ACTAGTGTAAGTCTGTAATGAGATTAATTCTGGAATTATATGTTAAATTTG
Found at i:54435 original size:51 final size:51
Alignment explanation
Indices: 54353--54793 Score: 467
Period size: 51 Copynumber: 8.7 Consensus size: 51
54343 GTCAGTGATA
* * * *
54353 AGTGATAAGTTTAGTT-CTGGAATTATATGTTAAATTTAACTGGTGTAAGAT-
1 AGTGATAAGTTCA-TTGCTGGAATAATGTGTTAAATTTAACTAGTGTAAG-TC
* ** *
54404 AGTGATAAGTTGATTAATGGAATAATGTGTTAAATTTCACT-GATGTAAGTC
1 AGTGATAAGTTCATTGCTGGAATAATGTGTTAAATTTAACTAG-TGTAAGTC
* * * * * * *
54455 ATTGATAAGTCCATTGATGAAATAATATGTTAAATTTAACCAGTGTAAGTG
1 AGTGATAAGTTCATTGCTGGAATAATGTGTTAAATTTAACTAGTGTAAGTC
* * * * *
54506 AGTGATAAGTTTATTGTTGGAATATTGTGTTCAATTCAACTAGTGTAAGTC
1 AGTGATAAGTTCATTGCTGGAATAATGTGTTAAATTTAACTAGTGTAAGTC
* * * * *
54557 ATTGATAAGTTCATTGGTAGAATAATGTGATAAATTTCACTAGTGTAAGTC
1 AGTGATAAGTTCATTGCTGGAATAATGTGTTAAATTTAACTAGTGTAAGTC
* * * *
54608 ATTGATAAGTTCATTGCTGGAATAATGTGTTAAATTT-ACTGGTGCAAGTT
1 AGTGATAAGTTCATTGCTGGAATAATGTGTTAAATTTAACTAGTGTAAGTC
* * * *
54658 AGTGATAAGTTTATTACTAGAATAATGTGTCAAATTTAACTAGTGTAAGTC
1 AGTGATAAGTTCATTGCTGGAATAATGTGTTAAATTTAACTAGTGTAAGTC
* * * * * *
54709 GGTGATATGTTCATTGCTAGAATAATGTGTTAAATTTCACTGGTGTAATTC
1 AGTGATAAGTTCATTGCTGGAATAATGTGTTAAATTTAACTAGTGTAAGTC
*
54760 AGTGATAAGTTCATTACTGGAATAATGTGTTAAA
1 AGTGATAAGTTCATTGCTGGAATAATGTGTTAAA
54794 GGTCTGTGAT
Statistics
Matches: 325, Mismatches: 60, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
50 46 0.14
51 278 0.86
52 1 0.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (51 bp):
AGTGATAAGTTCATTGCTGGAATAATGTGTTAAATTTAACTAGTGTAAGTC
Found at i:54435 original size:109 final size:109
Alignment explanation
Indices: 54244--54464 Score: 264
Period size: 109 Copynumber: 2.0 Consensus size: 109
54234 TAGGATAGTC
* * * * *
54244 AGTGATGAGTTTAGTGCTGGAATTATATGTTAAATTTGACTAGTGTAAGTTTGTAATGAGATTAA
1 AGTGATAAGTTTAGTGCTGGAATTATATGTTAAATTTAACTAGTGTAAGATAGTAATAAGATTAA
* * ** * *
54309 TTCTGGAATTATATGTTACGTTTGACTGGGGTAAGTCAGTGATA
66 TTATGGAATAATATGTTAAATTTCACTGAGGTAAGTCAGTGATA
* * * *
54353 AGTGATAAGTTTAGTTCTGGAATTATATGTTAAATTTAACTGGTGTAAGATAGTGATAAG-TTGA
1 AGTGATAAGTTTAGTGCTGGAATTATATGTTAAATTTAACTAGTGTAAGATAGTAATAAGATTAA
* * *
54417 TTAATGGAATAATGTGTTAAATTTCACTGATGTAAGTCATTGATA
66 TT-ATGGAATAATATGTTAAATTTCACTGAGGTAAGTCAGTGATA
54462 AGT
1 AGT
54465 CCATTGATGA
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
108 5 0.05
109 88 0.95
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (109 bp):
AGTGATAAGTTTAGTGCTGGAATTATATGTTAAATTTAACTAGTGTAAGATAGTAATAAGATTAA
TTATGGAATAATATGTTAAATTTCACTGAGGTAAGTCAGTGATA
Found at i:54569 original size:26 final size:25
Alignment explanation
Indices: 54544--54620 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
54534 GTTCAATTCA
54544 ACTAGTGTAAGTCATTGATAAGTTC
1 ACTAGTGTAAGTCATTGATAAGTTC
* * * *
54569 A-TTG-GTAGAATAATGTGATAAATTTC
1 ACTAGTGTA-AGTCAT-TGAT-AAGTTC
54595 ACTAGTGTAAGTCATTGATAAGTTC
1 ACTAGTGTAAGTCATTGATAAGTTC
54620 A
1 A
54621 TTGCTGGAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
23 3 0.08
24 6 0.15
25 11 0.28
26 10 0.26
27 6 0.15
28 3 0.08
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.36
Consensus pattern (25 bp):
ACTAGTGTAAGTCATTGATAAGTTC
Found at i:54734 original size:152 final size:151
Alignment explanation
Indices: 54353--54793 Score: 537
Period size: 152 Copynumber: 2.9 Consensus size: 151
54343 GTCAGTGATA
* * * * *
54353 AGTGATAAGTTTAGTTCTGGAATTATATGTTAAATTTAACTGGTGTAAGAT-AGTGATAAGTTGA
1 AGTGATAAGTTTA-TTCTGGAATAATGTGTCAAATTTAACTAGTGTAAG-TCAGTGATAAGTTCA
* * * * * *
54417 TTAATGGAATAATGTGTTAAATTTCACTGATGTAAGTCATTGATAAGTCCATTGATGAAATAATA
64 TTGATAGAATAATGTGTTAAATTTCACTG-TGTAAGTCATTGATAAGTTCATTGCTGGAATAATG
*
54482 TGTTAAATTTAACCAGTGTAAGTG
128 TGTTAAATTTAACCAGTGCAAGTG
* * * *
54506 AGTGATAAGTTTATTGTTGGAATATTGTGTTC-AATTCAACTAGTGTAAGTCATTGATAAGTTCA
1 AGTGATAAGTTTATT-CTGGAATAATGTG-TCAAATTTAACTAGTGTAAGTCAGTGATAAGTTCA
* *
54570 TTGGTAGAATAATGTGATAAATTTCACTAGTGTAAGTCATTGATAAGTTCATTGCTGGAATAATG
64 TTGATAGAATAATGTGTTAAATTTCACT-GTGTAAGTCATTGATAAGTTCATTGCTGGAATAATG
** *
54635 TGTTAAATTT-ACTGGTGCAAGTT
128 TGTTAAATTTAACCAGTGCAAGTG
* * *
54658 AGTGATAAGTTTATTACTAGAATAATGTGTCAAATTTAACTAGTGTAAGTCGGTGATATGTTCAT
1 AGTGATAAGTTTATT-CTGGAATAATGTGTCAAATTTAACTAGTGTAAGTCAGTGATAAGTTCAT
* * * *
54723 TGCTAGAATAATGTGTTAAATTTCACTGGTGTAATTCAGTGATAAGTTCATTACTGGAATAATGT
65 TGATAGAATAATGTGTTAAATTTCACT-GTGTAAGTCATTGATAAGTTCATTGCTGGAATAATGT
54788 GTTAAA
129 GTTAAA
54794 GGTCTGTGAT
Statistics
Matches: 248, Mismatches: 35, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
151 2 0.01
152 131 0.53
153 113 0.46
154 2 0.01
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (151 bp):
AGTGATAAGTTTATTCTGGAATAATGTGTCAAATTTAACTAGTGTAAGTCAGTGATAAGTTCATT
GATAGAATAATGTGTTAAATTTCACTGTGTAAGTCATTGATAAGTTCATTGCTGGAATAATGTGT
TAAATTTAACCAGTGCAAGTG
Found at i:54841 original size:38 final size:38
Alignment explanation
Indices: 54757--54841 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
54747 ACTGGTGTAA
* *
54757 TTCAGTGATAAGTTCATTACTGGAATAATGTGTTAAAG
1 TTCAGTGATAAGTTCACTACTGGAATAATGTGTTAAAC
* * *
54795 GTCTGTGATAAGTTCACTACTGGAATTATGTGTTAAAC
1 TTCAGTGATAAGTTCACTACTGGAATAATGTGTTAAAC
54833 TTCAGTGAT
1 TTCAGTGAT
54842 GGAATTAGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (38 bp):
TTCAGTGATAAGTTCACTACTGGAATAATGTGTTAAAC
Found at i:55678 original size:36 final size:36
Alignment explanation
Indices: 55631--55780 Score: 212
Period size: 36 Copynumber: 4.2 Consensus size: 36
55621 TGATATTCCC
*
55631 ATGCATGATATACATGCACTTGCTACTGATGATTAT
1 ATGCATGATATACATGCGCTTGCTACTGATGATTAT
* * *
55667 ATGCATGATATACATGCTCTTGATATTGATGATTAT
1 ATGCATGATATACATGCGCTTGCTACTGATGATTAT
* * * *
55703 ATGCATGATATACATGTGTTTACTACTGGTGATTAT
1 ATGCATGATATACATGCGCTTGCTACTGATGATTAT
*
55739 ATGCATGATATACATG-GCTTGCTGCTGATGATTAT
1 ATGCATGATATACATGCGCTTGCTACTGATGATTAT
55774 ATGCATG
1 ATGCATG
55781 GTCTTTTACC
Statistics
Matches: 100, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 22 0.22
36 78 0.78
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (36 bp):
ATGCATGATATACATGCGCTTGCTACTGATGATTAT
Found at i:57206 original size:6 final size:6
Alignment explanation
Indices: 57195--57227 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
57185 TAAGGTTCAT
*
57195 ATTGAC ATTGAC ATTGAC ATTGAC TTTGAC ATT
1 ATTGAC ATTGAC ATTGAC ATTGAC ATTGAC ATT
57228 TTGACTGACG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (6 bp):
ATTGAC
Found at i:57427 original size:2 final size:2
Alignment explanation
Indices: 57420--57468 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
57410 ATTTTTGTAA
57420 AT AT 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 AT AT
57462 AT AT AT A
1 AT AT AT A
57469 ATAAAGATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59236 original size:59 final size:60
Alignment explanation
Indices: 59150--59303 Score: 199
Period size: 59 Copynumber: 2.6 Consensus size: 60
59140 CAAAATTTGG
* * *
59150 GGACCAATTTAGAAA-GAGGGTCATAGTTTAGGGATAAAATTAGAATGTTCAAGAG-TTAA
1 GGACTAATTTA-AAATGAGGGTCATAGTTTAGGGATAAAATTAGAATATTCAAAAGTTTAA
* * * *
59209 GGA-TAGATTTAAAATGAGAGTCATAGTTT-GGGATGAAATTGGAATATTCAAAAGTTTAG
1 GGACTA-ATTTAAAATGAGGGTCATAGTTTAGGGATAAAATTAGAATATTCAAAAGTTTAA
59268 GGACTAATTTAAAATGAGGGTCATAGTTTAGGGATA
1 GGACTAATTTAAAATGAGGGTCATAGTTTAGGGATA
59304 TATGATGTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
58 25 0.31
59 49 0.60
60 7 0.09
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (60 bp):
GGACTAATTTAAAATGAGGGTCATAGTTTAGGGATAAAATTAGAATATTCAAAAGTTTAA
Found at i:69617 original size:3 final size:3
Alignment explanation
Indices: 69609--69700 Score: 157
Period size: 3 Copynumber: 30.7 Consensus size: 3
69599 TTAAAGGTAT
*
69609 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
69657 ATA ATA ATA ATA ATA ATA ATC ATA ATC ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
69701 CAAGAACATG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:84475 original size:31 final size:31
Alignment explanation
Indices: 84433--84501 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
84423 GAGTTTGGTT
84433 AAAATC-CTGCCTTGTCATTTTAGAGATGTG
1 AAAATCTCTGCCTTGTCATTTTAGAGATGTG
*
84463 AAAATCTCTGCCTTGTCATTTTAGAGTTGTG
1 AAAATCTCTGCCTTGTCATTTTAGAGATGTG
*
84494 AAATTCTC
1 AAAATCTC
84502 AAAATATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 6 0.17
31 30 0.83
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.39
Consensus pattern (31 bp):
AAAATCTCTGCCTTGTCATTTTAGAGATGTG
Found at i:92477 original size:7 final size:7
Alignment explanation
Indices: 92465--92522 Score: 82
Period size: 7 Copynumber: 8.1 Consensus size: 7
92455 CCTTATTCTC
92465 TTTCTTT
1 TTTCTTT
92472 TTTCTTT
1 TTTCTTT
92479 TTTCTTT
1 TTTCTTT
92486 TTTCTTT
1 TTTCTTT
*
92493 CTTCTTT
1 TTTCTTT
92500 TTTCATTT
1 TTTC-TTT
92508 TTTCCTTT
1 TTT-CTTT
92516 TTT-TTT
1 TTTCTTT
92522 T
1 T
92523 GTTTGAACCA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
6 4 0.09
7 30 0.64
8 12 0.26
9 1 0.02
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTCTTT
Found at i:95822 original size:18 final size:18
Alignment explanation
Indices: 95799--95845 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
95789 AACCCCTTGG
*
95799 GTATCGATACTCACCTAA
1 GTATCGATACCCACCTAA
95817 GTATCGATACCCACCTAA
1 GTATCGATACCCACCTAA
95835 GTATCGATACC
1 GTATCGATACC
95846 AAATTTAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.26
Consensus pattern (18 bp):
GTATCGATACCCACCTAA
Found at i:96026 original size:21 final size:21
Alignment explanation
Indices: 96002--96053 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
95992 TAGACCCCGA
96002 GTATCGGTACTCCTTAAAGGG
1 GTATCGGTACTCCTTAAAGGG
96023 GTATCGAG-ACTCCTTAAAGGG
1 GTATCG-GTACTCCTTAAAGGG
*
96044 GTATCAGTAC
1 GTATCGGTAC
96054 CTACCCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
GTATCGGTACTCCTTAAAGGG
Found at i:108546 original size:30 final size:31
Alignment explanation
Indices: 108511--108584 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
108501 TGACGTTCAA
108511 TGTAATTTATAAAAAAAGTT-TGT-CTTATAT
1 TGTAATTTATAAAAAAAGTTCTGTCCTT-TAT
* *
108541 TGTAA-TT-TACAAAAGGTTCTGTCCTTTAT
1 TGTAATTTATAAAAAAAGTTCTGTCCTTTAT
108570 TGTAATTTATAAAAA
1 TGTAATTTATAAAAA
108585 GTTATGTCCT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 9 0.24
29 13 0.35
30 10 0.27
31 5 0.14
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.45
Consensus pattern (31 bp):
TGTAATTTATAAAAAAAGTTCTGTCCTTTAT
Found at i:108570 original size:29 final size:29
Alignment explanation
Indices: 108523--108595 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
108513 TAATTTATAA
108523 AAAAAGTT-TGT-CTTATATTGTAATTTAC
1 AAAAAGTTATGTCCTT-TATTGTAATTTAC
* * *
108551 AAAAGGTTCTGTCCTTTATTGTAATTTAT
1 AAAAAGTTATGTCCTTTATTGTAATTTAC
108580 AAAAAGTTATGTCCTT
1 AAAAAGTTATGTCCTT
108596 CAATGTAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 7 0.18
29 29 0.74
30 3 0.08
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (29 bp):
AAAAAGTTATGTCCTTTATTGTAATTTAC
Found at i:108602 original size:29 final size:28
Alignment explanation
Indices: 108506--108602 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 28
108496 AGTTTTGACG
108506 TTCAATGTAATTTATAAAAAAAGTTTGT-C
1 TTCAATGTAATTTAT--AAAAAGTTTGTCC
* *
108535 TT-ATATTGTAATTTACAAAAGGTTCTGTCC
1 TTCA-A-TGTAATTTATAAAAAGTT-TGTCC
* *
108565 TTTATTGTAATTTATAAAAAGTTATGTCC
1 TTCAATGTAATTTATAAAAAGTT-TGTCC
108594 TTCAATGTA
1 TTCAATGTA
108603 GAGAATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 8 0.15
29 34 0.62
30 12 0.22
31 1 0.02
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.44
Consensus pattern (28 bp):
TTCAATGTAATTTATAAAAAGTTTGTCC
Found at i:108657 original size:29 final size:29
Alignment explanation
Indices: 108615--108712 Score: 155
Period size: 29 Copynumber: 3.4 Consensus size: 29
108605 GAATTATTTC
108615 TTTATTGTAATTTATATAAAAAATTGAAA
1 TTTATTGTAATTTATATAAAAAATTGAAA
108644 TTTATTGTAATTTATATAAAAAATTGAAA
1 TTTATTGTAATTTATATAAAAAATTGAAA
* *
108673 TTTATTGTAATTTATAT-GAAAATAG-AA
1 TTTATTGTAATTTATATAAAAAATTGAAA
108700 TATTATTGTAATT
1 T-TTATTGTAATT
108713 GTAATTTTGA
Statistics
Matches: 66, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
27 3 0.05
28 17 0.26
29 46 0.70
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (29 bp):
TTTATTGTAATTTATATAAAAAATTGAAA
Found at i:110883 original size:20 final size:18
Alignment explanation
Indices: 110840--110880 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
110830 TATTTAACTC
*
110840 AATCTATATAATTTAATA
1 AATCTATATAATTTAAGA
*
110858 AATCTATATAGTTTAAGA
1 AATCTATATAATTTAAGA
110876 AATCT
1 AATCT
110881 CTAACTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (18 bp):
AATCTATATAATTTAAGA
Found at i:111752 original size:18 final size:18
Alignment explanation
Indices: 111713--111754 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
111703 CGTAACCGTT
*
111713 TTTTTAAAAAGAGCGTCA
1 TTTTTAAAAACAGCGTCA
111731 -TTTTAAAAACCA-CGTCA
1 TTTTTAAAAA-CAGCGTCA
111748 TTTTTAA
1 TTTTTAA
111755 TTATTTCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (18 bp):
TTTTTAAAAACAGCGTCA
Found at i:112268 original size:21 final size:22
Alignment explanation
Indices: 112244--112284 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
112234 TAAAAACTTA
112244 AGGTA-CTTAAATAATAAAAAT
1 AGGTAGCTTAAATAATAAAAAT
* *
112265 AGGTAGTTTAAATACTAAAA
1 AGGTAGCTTAAATAATAAAA
112285 TAATAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.54, C:0.05, G:0.12, T:0.29
Consensus pattern (22 bp):
AGGTAGCTTAAATAATAAAAAT
Found at i:112286 original size:30 final size:29
Alignment explanation
Indices: 112247--112326 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
112237 AAACTTAAGG
* * **
112247 TACTTAAATAATAAAAATAGGTAGTTTAAA
1 TACTAAAATAATAAAAATA-GAAAATTAAA
*
112277 TACTAAAATAATAAAAAATAGAAAATTAAG
1 TACTAAAATAAT-AAAAATAGAAAATTAAA
112307 TAACTAAAATAATAAAAATA
1 T-ACTAAAATAATAAAAATA
112327 TATAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
30 25 0.58
31 18 0.42
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (29 bp):
TACTAAAATAATAAAAATAGAAAATTAAA
Found at i:113989 original size:22 final size:22
Alignment explanation
Indices: 113946--114011 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
113936 ATGTAGCATT
*
113946 ATTATTAATAATAACA-ACAATA
1 ATTATTAATAATAA-ATATAATA
*
113968 CTTATTAATAATAAATATAATA
1 ATTATTAATAATAAATATAATA
* *
113990 ATAAATAATAATAAATATAATA
1 ATTATTAATAATAAATATAATA
114012 TAATATGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 1 0.03
22 37 0.97
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTATTAATAATAAATATAATA
Found at i:113990 original size:12 final size:12
Alignment explanation
Indices: 113973--114059 Score: 65
Period size: 14 Copynumber: 7.2 Consensus size: 12
113963 CAATACTTAT
113973 TAATAATAAATA
1 TAATAATAAATA
113985 TAATAAT-AA-A
1 TAATAATAAATA
113995 TAATAATAAATA
1 TAATAATAAATA
114007 TAAT-AT-AATA
1 TAATAATAAATA
* *
114017 TGATATATATATA
1 TAATA-ATAAATA
*
114030 TATATATATATATA
1 TA-ATA-ATAAATA
*
114044 TATATATATATATA
1 TA-ATA-ATAAATA
114058 TA
1 TA
114060 TATATATTAG
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
10 15 0.23
11 6 0.09
12 14 0.21
13 4 0.06
14 27 0.41
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (12 bp):
TAATAATAAATA
Found at i:114017 original size:10 final size:11
Alignment explanation
Indices: 113982--114066 Score: 92
Period size: 10 Copynumber: 8.2 Consensus size: 11
113972 TTAATAATAA
113982 ATATAATA-AT
1 ATATAATATAT
* *
113992 AAATAATAATAA
1 ATATAAT-ATAT
114004 ATATAATATA-
1 ATATAATATAT
*
114014 ATATGATATAT
1 ATATAATATAT
114025 ATAT-ATATAT
1 ATATAATATAT
114035 ATAT-ATATAT
1 ATATAATATAT
114045 ATAT-ATATAT
1 ATATAATATAT
114055 ATAT-ATATAT
1 ATATAATATAT
114065 AT
1 AT
114067 TAGATCCCAA
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
10 53 0.78
11 8 0.12
12 7 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
ATATAATATAT
Found at i:114026 original size:2 final size:2
Alignment explanation
Indices: 114004--114066 Score: 103
Period size: 2 Copynumber: 32.0 Consensus size: 2
113994 ATAATAATAA
114004 AT AT A- AT AT A- AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
114045 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
114067 TAGATCCCAA
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.03
2 54 0.93
3 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:114542 original size:136 final size:136
Alignment explanation
Indices: 114305--114783 Score: 765
Period size: 136 Copynumber: 3.6 Consensus size: 136
114295 GACTTGAAAG
* * * * *
114305 GAACAAGTTCTTTTCATTATGAAC-T-TTCTCCAT-TA--AGATGGGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* * ** **
114365 CTTC--TAGAAATGTCAATTTCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
114428 TAGGTC
131 TAGGTC
*
114434 GAACAAGCTCTTCCCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
114499 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
114564 TAGGTC
131 TAGGTC
114570 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
*
114635 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGCCGTGAATCGAGTGA
66 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
114700 TAGGTC
131 TAGGTC
*
114706 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
* *
114771 CTCTATTGAAAAT
66 CTCCATTGGAAAT
114784 ATTGATGCAA
Statistics
Matches: 326, Mismatches: 17, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
129 21 0.06
130 1 0.00
131 7 0.02
132 2 0.01
134 26 0.08
136 269 0.83
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGGAAATGTCAATCCCTCAAGCGAGGCATCACTGATTCGAAATGTCGTGAATCGAGTGA
TAGGTC
Found at i:114859 original size:88 final size:92
Alignment explanation
Indices: 114703--114877 Score: 268
Period size: 88 Copynumber: 1.9 Consensus size: 92
114693 CGAGTGATAG
*
114703 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGA
1 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTCTTCTCATTATGA
*
114768 ACTCTCTATTGAAAATATTGATGCAAA
66 ACTCTCCATTGAAAATATTGATGCAAA
* * *
114795 GTCGAACAAGTTCTTCTCATTGTGAACTT-TT-T-CTTCT-TCGGATGAATTCTTCTCATTATGA
1 GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTCTTCTCATTATGA
*
114856 ACTCTCCATTGAAAATGTTGAT
66 ACTCTCCATTGAAAATATTGAT
114878 CCACCTGCTT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
88 43 0.56
89 4 0.05
90 1 0.01
91 2 0.03
92 27 0.35
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (92 bp):
GTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAATTCTTCTCATTATGA
ACTCTCCATTGAAAATATTGATGCAAA
Found at i:115880 original size:7 final size:8
Alignment explanation
Indices: 115868--115920 Score: 67
Period size: 7 Copynumber: 6.8 Consensus size: 8
115858 TCTCTTCGTT
115868 TTTTTTC-
1 TTTTTTCA
115875 TTTTTTCA
1 TTTTTTCA
115883 TTTTTTTCA
1 -TTTTTTCA
115892 -TTTTTCA
1 TTTTTTCA
115899 TTTTTTTC-
1 -TTTTTTCA
115907 TTTTTTCA
1 TTTTTTCA
115915 TTTTTT
1 TTTTTT
115921 TCTTCAAGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
7 21 0.51
8 6 0.15
9 14 0.34
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCA
Found at i:115886 original size:16 final size:16
Alignment explanation
Indices: 115867--115924 Score: 107
Period size: 16 Copynumber: 3.6 Consensus size: 16
115857 TTCTCTTCGT
115867 TTTTTTTCTTTTTTCA
1 TTTTTTTCTTTTTTCA
*
115883 TTTTTTTCATTTTTCA
1 TTTTTTTCTTTTTTCA
115899 TTTTTTTCTTTTTTCA
1 TTTTTTTCTTTTTTCA
115915 TTTTTTTCTT
1 TTTTTTTCTT
115925 CAAGCATAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTTTTCA
Found at i:130887 original size:200 final size:200
Alignment explanation
Indices: 130539--130912 Score: 466
Period size: 200 Copynumber: 1.9 Consensus size: 200
130529 TCGAATTTGA
* * * ** *
130539 AAGCTTTGGTCGACATATAGCTCTTTTGGACTTAAGCTATGCAAGATCTGGGCTAAAAAGTAGTT
1 AAGCTTTGGTCGACAAATAACTCTTCTCCACTTAAGCTATGCAAAATCTGGGCTAAAAAGTAGTT
** * * *
130604 TGTTGTTGCTAAATAACATCCGATTTAGGCCTTCTTTTAGACTTGAAGACTTTGGTTTGAATTTT
66 CCTCGTTGCTAAATAACACCCGATTTAGGCCTTCTTATAGACTTGAAGACTTTGGTTTGAATTTT
* * * *
130669 AACCGGAAGGTAGTTCCTCGTTGCTACC-TGCGATTAATGTGCTCCTGAGTTGAATTAAATCAAA
131 AACCGAAAGGTAGTTCCTCATTGCCACCATGCGATCAATGTGCTCCTGAGTTGAATTAAATCAAA
130733 CTATG
196 CTATG
** *
130738 AAGCTTTGGTCGACAAATAACTCTTCTCCACTTAAGCTATGTCAAAATCTGGGCTGGGATA-TAG
1 AAGCTTTGGTCGACAAATAACTCTTCTCCACTTAAGCTATG-CAAAATCTGGGCT-AAAAAGTAG
** * *
130802 TTCCTCGTTGCTAAATCGCACCCGATTTGGGCCTTCTTATAGGCTTGAAGAAC-TTGGTTTGAAT
64 TTCCTCGTTGCTAAATAACACCCGATTTAGGCCTTCTTATAGACTTGAAG-ACTTTGGTTTGAAT
* * * *
130866 TTTAACCTAAATGTGGTTCCTCATTGCCACCATGGGATCAATGTGCT
128 TTTAACCGAAAGGTAGTTCCTCATTGCCACCATGCGATCAATGTGCT
130913 TTCAAGTTGA
Statistics
Matches: 145, Mismatches: 26, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
199 36 0.25
200 92 0.63
201 17 0.12
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (200 bp):
AAGCTTTGGTCGACAAATAACTCTTCTCCACTTAAGCTATGCAAAATCTGGGCTAAAAAGTAGTT
CCTCGTTGCTAAATAACACCCGATTTAGGCCTTCTTATAGACTTGAAGACTTTGGTTTGAATTTT
AACCGAAAGGTAGTTCCTCATTGCCACCATGCGATCAATGTGCTCCTGAGTTGAATTAAATCAAA
CTATG
Found at i:131103 original size:71 final size:71
Alignment explanation
Indices: 130997--131178 Score: 179
Period size: 71 Copynumber: 2.5 Consensus size: 71
130987 TGGATGAATC
* * * * * *
130997 CCCTTTGTGGGAAAGACAGGTGAGATGAATCCCCTTCACGGTTTAAGTAAGTCTTGATTAGTTGG
1 CCCTTCGTGAGAAAG-CAGGTGAGATGACTCCCCTTCAAGGTTTAACTAAGTCTTGATTAGTTGA
131062 ATGAC-A
65 ATGACTA
* * ** **
131068 CCCTTCGTGAGAAAGCTAGGTGAGATGACTTCCCTTTAAGGTTTAACTTGGTCTTGATTCTTTGA
1 CCCTTCGTGAGAAAGC-AGGTGAGATGACTCCCCTTCAAGGTTTAACTAAGTCTTGATTAGTTGA
131133 ATGACTA
65 ATGACTA
* *
131140 CCCTTCAT-AGGAAAGGCCAGGTGAGACGACTCCCCTTCA
1 CCCTTCGTGA-GAAA-G-CAGGTGAGATGACTCCCCTTCA
131179 TGAGTCTAAT
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
70 1 0.01
71 57 0.63
72 12 0.13
73 19 0.21
74 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (71 bp):
CCCTTCGTGAGAAAGCAGGTGAGATGACTCCCCTTCAAGGTTTAACTAAGTCTTGATTAGTTGAA
TGACTA
Found at i:134297 original size:53 final size:53
Alignment explanation
Indices: 134216--134369 Score: 157
Period size: 53 Copynumber: 2.9 Consensus size: 53
134206 AAAATCTATA
* * *
134216 CAGAAACCACAGAAAATGATGAATGTGTTGTAAAATGCTTTACGAACATCTGAC
1 CAGAAGCCACA-AAAAAGATGAATGTGTTGTAAAATGCTTTACGAACATCCGAC
* * **
134270 CAGAAGCCACAAAAAAGATGAATGTGTTATCAAAA-GCTTTACGAAAATCCGGG
1 CAGAAGCCACAAAAAAGATGAATGTGTTGT-AAAATGCTTTACGAACATCCGAC
* * * * * *
134323 CAGAAGCCACGAGAAAGGATGAATGTATTGTCACATGTTTTACGAAC
1 CAGAAGCCAC-AAAAAAGATGAATGTGTTGTAAAATGCTTTACGAAC
134370 CAGTGATTAT
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
53 43 0.52
54 39 0.48
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (53 bp):
CAGAAGCCACAAAAAAGATGAATGTGTTGTAAAATGCTTTACGAACATCCGAC
Found at i:134367 original size:54 final size:53
Alignment explanation
Indices: 134216--134368 Score: 171
Period size: 54 Copynumber: 2.8 Consensus size: 53
134206 AAAATCTATA
* * * *
134216 CAGAAACCACAGAAAATGATGAATGTGTTGTAAAATGCTTTACGAACATCTGAC
1 CAGAAGCCACAGAAAA-GATGAATGTGTTGTCAAATGCTTTACGAAAATCCGAC
* * * **
134270 CAGAAGCCACAAAAAAGATGAATGTGTTATCAAAAGCTTTACGAAAATCCGGG
1 CAGAAGCCACAGAAAAGATGAATGTGTTGTCAAATGCTTTACGAAAATCCGAC
* * * *
134323 CAGAAGCCACGAGAAAGGATGAATGTATTGTCACATGTTTTACGAA
1 CAGAAGCCAC-AGAAAAGATGAATGTGTTGTCAAATGCTTTACGAA
134369 CCAGTGATTA
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 40 0.49
54 42 0.51
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (53 bp):
CAGAAGCCACAGAAAAGATGAATGTGTTGTCAAATGCTTTACGAAAATCCGAC
Found at i:134754 original size:22 final size:22
Alignment explanation
Indices: 134729--134803 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
134719 CTACATTCTC
134729 CAAAGATGATAGATTCTCTCTT
1 CAAAGATGATAGATTCTCTCTT
* *
134751 CAAAGATGATATATTCTCTCTC
1 CAAAGATGATAGATTCTCTCTT
*
134773 CAAAGATGATAGATTCTCTTTT
1 CAAAGATGATAGATTCTCTCTT
134795 CAAAGATGA
1 CAAAGATGA
134804 AAGCTTTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
CAAAGATGATAGATTCTCTCTT
Found at i:135172 original size:17 final size:17
Alignment explanation
Indices: 135150--135184 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
135140 TACATTTCAT
135150 TGCATTCAAACATGAAG
1 TGCATTCAAACATGAAG
135167 TGCATTCAAACATGAAG
1 TGCATTCAAACATGAAG
135184 T
1 T
135185 TTTACAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (17 bp):
TGCATTCAAACATGAAG
Found at i:135531 original size:45 final size:45
Alignment explanation
Indices: 135466--135815 Score: 583
Period size: 45 Copynumber: 7.8 Consensus size: 45
135456 CTATTTCCCA
* *
135466 CATCTGTAAGCCCTTTAGTGCATGATGTTATCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
135511 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
135556 CATCTGTAAGCCCTTCAGTGCATTATGTTTTCAAAACTTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
135601 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACTTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * **
135646 CATATGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGATT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
135691 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
135736 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCCTTCGGAT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-CCTTCGGGT
135782 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
135816 CATTTTCATC
Statistics
Matches: 285, Mismatches: 19, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
45 244 0.86
46 41 0.14
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:135941 original size:3 final size:3
Alignment explanation
Indices: 135933--136014 Score: 96
Period size: 3 Copynumber: 27.0 Consensus size: 3
135923 CAATTTGCTT
* *
135933 TTA TTA TTA TTA TTA TTTA TT- TTA TTA TTG TTA TTA TTA -TA TACA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
135978 TTA TTA TTA TTA TTA TTG TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
136015 AATAAATATT
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
2 4 0.06
3 56 0.82
4 8 0.12
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:137534 original size:21 final size:22
Alignment explanation
Indices: 137488--137532 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
137478 TCATTGTTTA
137488 TTTATAT-TTTAATTTTATATG
1 TTTATATATTTAATTTTATATG
137509 TTTATATATTTAATTATTAT-TG
1 TTTATATATTTAATT-TTATATG
137531 TT
1 TT
137533 ATTATTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTATATATTTAATTTTATATG
Found at i:137926 original size:9 final size:9
Alignment explanation
Indices: 137908--137936 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
137898 AATATCTTAT
137908 TTAT-AAAA
1 TTATAAAAA
137916 TTATAAAAA
1 TTATAAAAA
137925 TTATAAAAA
1 TTATAAAAA
137934 TTA
1 TTA
137937 ATATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
TTATAAAAA
Found at i:143788 original size:3 final size:3
Alignment explanation
Indices: 143780--143805 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
143770 TTTATTTAAT
143780 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
143806 TTAAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.