Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, 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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 18 of 26
Found at i:7235494 original size:14 final size:14
Alignment explanation
Indices: 7235472--7235513 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
7235462 TTCGATAGAA
7235472 AAGAGGAAAAAAAGG
1 AAGAGGAAAAAAA-G
*
7235487 AA-AGGAAAAGAAG
1 AAGAGGAAAAAAAG
7235500 AAGAGGAGAAAAAA
1 AAGAGGA-AAAAAA
7235514 ATGGGCGAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 3 0.13
14 13 0.57
15 7 0.30
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (14 bp):
AAGAGGAAAAAAAG
Found at i:7236182 original size:20 final size:20
Alignment explanation
Indices: 7236157--7236221 Score: 130
Period size: 20 Copynumber: 3.2 Consensus size: 20
7236147 CAAATTTCAT
7236157 TATGTTTATATATATGAACA
1 TATGTTTATATATATGAACA
7236177 TATGTTTATATATATGAACA
1 TATGTTTATATATATGAACA
7236197 TATGTTTATATATATGAACA
1 TATGTTTATATATATGAACA
7236217 TATGT
1 TATGT
7236222 CTATCTCCGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (20 bp):
TATGTTTATATATATGAACA
Found at i:7248101 original size:18 final size:16
Alignment explanation
Indices: 7248048--7248101 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 16
7248038 ATTTTGAACT
7248048 TTAATTTTTTTAATGAA
1 TTAATTTTTTTAAT-AA
*
7248065 TTAATTTTAATTTATTAA
1 TTAATTTT--TTTAATAA
7248083 TTAAATTTTTGTTAATAA
1 TT-AATTTTT-TTAATAA
7248101 T
1 T
7248102 ATATATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 9 0.29
18 11 0.35
19 11 0.35
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
TTAATTTTTTTAATAA
Found at i:7248954 original size:15 final size:17
Alignment explanation
Indices: 7248924--7248956 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
7248914 TATTTTGTGT
7248924 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
7248941 TAAC-TTAT-AAAATTA
1 TAACATTATAAAAATTA
7248956 T
1 T
7248957 TAATTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:7254220 original size:2 final size:2
Alignment explanation
Indices: 7254213--7254243 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
7254203 CTGGCAAATT
*
7254213 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7254244 CCATGTCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7256774 original size:27 final size:25
Alignment explanation
Indices: 7256739--7256881 Score: 92
Period size: 28 Copynumber: 5.2 Consensus size: 25
7256729 TGCTATGTAC
7256739 AAATATGTTACACGTCATGTTAAGAA
1 AAATATGTTACACGTCATGTTAA-AA
* *
7256765 AAATACTGTTGTTGCACGTCATG-TACAA
1 AAATA----TGTTACACGTCATGTTAAAA
* *
7256793 AAACATGTTACACGCCATGGTTAAAA
1 AAATATGTTACACGTCAT-GTTAAAA
*
7256819 AAA-AGTTGTTACACGTTATGTTAAAAAA
1 AAATA--TGTTACACGTCATGTT--AAAA
*
7256847 AAATATTGTTATTACACGTCATGTTGAAA
1 AAATA-TG---TTACACGTCATGTTAAAA
7256876 AAATAT
1 AAATAT
7256882 TATTATTACA
Statistics
Matches: 93, Mismatches: 10, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
24 11 0.12
25 2 0.02
26 15 0.16
27 11 0.12
28 17 0.18
29 11 0.12
30 13 0.14
31 13 0.14
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (25 bp):
AAATATGTTACACGTCATGTTAAAA
Found at i:7256865 original size:31 final size:29
Alignment explanation
Indices: 7256827--7256906 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
7256817 AAAAAAGTTG
* *
7256827 TTACACGTTATGTTAAAAAAAAATATTGTTA
1 TTACACGTCATGTT--AAAAAAATATTATTA
*
7256858 TTACACGTCATGTTGAAAAAATATTATTA
1 TTACACGTCATGTTAAAAAAATATTATTA
* *
7256887 TTACACGTCATATTCAAAAA
1 TTACACGTCATGTTAAAAAA
7256907 CATTTTGTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 31 0.70
31 13 0.30
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (29 bp):
TTACACGTCATGTTAAAAAAATATTATTA
Found at i:7256876 original size:29 final size:29
Alignment explanation
Indices: 7256844--7256916 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
7256834 TTATGTTAAA
* *
7256844 AAAAAATATTGTTATTACACGTCATGTTG
1 AAAAAATATTGTTATTACACGTCATATTC
*
7256873 AAAAAATATTATTATTACACGTCATATTC
1 AAAAAATATTGTTATTACACGTCATATTC
*
7256902 AAAAACATTTTGTTA
1 AAAAA-ATATTGTTA
7256917 CACTTTACTG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 31 0.82
30 7 0.18
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.38
Consensus pattern (29 bp):
AAAAAATATTGTTATTACACGTCATATTC
Found at i:7257313 original size:22 final size:22
Alignment explanation
Indices: 7257272--7257319 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
7257262 CAAAGTGCTG
7257272 GAAAGAAAAATTTGAAAGCATGA
1 GAAAGAAAAATTTGAAAGCAT-A
* *
7257295 GAAAGAGAAA-TTGATAGCATA
1 GAAAGAAAAATTTGAAAGCATA
7257316 GAAA
1 GAAA
7257320 ACGAATGCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 9 0.39
23 9 0.39
ACGTcount: A:0.56, C:0.04, G:0.23, T:0.17
Consensus pattern (22 bp):
GAAAGAAAAATTTGAAAGCATA
Found at i:7263102 original size:6 final size:6
Alignment explanation
Indices: 7263093--7263122 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
7263083 TGATTATTTT
7263093 TTTCTC TTTCTC TTTCTC TTTTCTC TTTCT
1 TTTCTC TTTCTC TTTCTC -TTTCTC TTTCT
7263123 TTTGCAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTCTC
Found at i:7263117 original size:13 final size:12
Alignment explanation
Indices: 7263093--7263122 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
7263083 TGATTATTTT
7263093 TTTCTCTTTCTC
1 TTTCTCTTTCTC
7263105 TTTCTCTTTTCTC
1 TTTCTC-TTTCTC
7263118 TTTCT
1 TTTCT
7263123 TTTGCAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTCTCTTTCTC
Found at i:7265155 original size:208 final size:208
Alignment explanation
Indices: 7264794--7265172 Score: 516
Period size: 208 Copynumber: 1.8 Consensus size: 208
7264784 GTGTGACTGC
* * * *
7264794 TATTTTGGCATAACATAAGTGGATATTAGGCATTGCATGACTTATTATTAAGTATTGTGAGACTG
1 TATTTTGGCATAACATAAGTAGATATTAGGCATTGCATGACTTATTATTAAGTATTCTAAGACTA
* * * *
7264859 GCATATAGGTATTATGTGAATTGTGCAATGCATATCTTGTTTTAAGACATTTCTTGATTACTTCT
66 GCATATAGGTACTACGTGAATTGTGCAATGCACATCTTGTTTTAAGACATTTCTTGACTACTTCT
* *
7264924 TTAACATTACGTGACTGGTTGTTATGTATTTCGTGAC-TTGTTATGTATTGTGTGACATTGGGTC
131 TTAACATTACGTGACTAGTTGTTA-GTATTGCGTGACATTGTTATGTATTGTGTGACATTGGGTC
7264988 AATGCCTGACTGGT
195 AATGCCTGACTGGT
* * * *
7265002 TATTTTGGCATAACGTGAGTAGATATTAGGCATTG-AGTGACTTATTGTTAGGTATTCTAAGACT
1 TATTTTGGCATAACATAAGTAGATATTAGGCATTGCA-TGACTTATTATTAAGTATTCTAAGACT
* *
7265066 AGCTTATAGG-AGCTACGTGAATTGTGCAATGCACATCTTGTTTTGAGACATTTCTTGACTACTT
65 AGCATATAGGTA-CTACGTGAATTGTGCAATGCACATCTTGTTTTAAGACATTTCTTGACTACTT
* *
7265130 -TTTAGGCCTTGA-GTGACTAGTTGTTAGTATTGCGTGACATTGT
129 CTTTA-ACATT-ACGTGACTAGTTGTTAGTATTGCGTGACATTGT
7265173 GTCAATACCT
Statistics
Matches: 148, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
207 17 0.11
208 130 0.88
209 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (208 bp):
TATTTTGGCATAACATAAGTAGATATTAGGCATTGCATGACTTATTATTAAGTATTCTAAGACTA
GCATATAGGTACTACGTGAATTGTGCAATGCACATCTTGTTTTAAGACATTTCTTGACTACTTCT
TTAACATTACGTGACTAGTTGTTAGTATTGCGTGACATTGTTATGTATTGTGTGACATTGGGTCA
ATGCCTGACTGGT
Found at i:7267313 original size:84 final size:84
Alignment explanation
Indices: 7267172--7267339 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
7267162 ATATATCTAA
*
7267172 TTGCATTTTGCATTGGCCACATGGAGGATGAAAAGGCTCAATCCTGGTTCCTTACCTAAATGTGT
1 TTGCATTTTGCATTGGCCACATGGAGGATGAAAAGGCTCAATCATGGTTCCTTACCTAAATGTGT
7267237 CATGTGATTAGTTGTCCTG
66 CATGTGATTAGTTGTCCTG
7267256 TTGCATTTTGCATTGGCCACATGGAGGATGAAAAGGCTCAATCATGGTTCCTTACCTAAATGTGT
1 TTGCATTTTGCATTGGCCACATGGAGGATGAAAAGGCTCAATCATGGTTCCTTACCTAAATGTGT
7267321 CATGTGATTAGTTGTCCTG
66 CATGTGATTAGTTGTCCTG
7267340 AAAATGCAAT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (84 bp):
TTGCATTTTGCATTGGCCACATGGAGGATGAAAAGGCTCAATCATGGTTCCTTACCTAAATGTGT
CATGTGATTAGTTGTCCTG
Found at i:7268242 original size:23 final size:23
Alignment explanation
Indices: 7268210--7268277 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
7268200 TGAACCATAT
*
7268210 TCACACAATGACCTATCAACCAC
1 TCACGCAATGACCTATCAACCAC
7268233 -CAACGCAATGACCTATCAACCAC
1 TC-ACGCAATGACCTATCAACCAC
* *
7268256 TCACGCAATGACATATTAACCA
1 TCACGCAATGACCTATCAACCA
7268278 GTTACACAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.40, C:0.35, G:0.07, T:0.18
Consensus pattern (23 bp):
TCACGCAATGACCTATCAACCAC
Found at i:7268287 original size:23 final size:23
Alignment explanation
Indices: 7268210--7268287 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
7268200 TGAACCATAT
*
7268210 TCACACAATGACCTATCAACCAC
1 TCACACAATGACATATCAACCAC
* *
7268233 -CAACGCAATGACCTATCAACCAC
1 TC-ACACAATGACATATCAACCAC
* * *
7268256 TCACGCAATGACATATTAACCAG
1 TCACACAATGACATATCAACCAC
*
7268279 TTACACAAT
1 TCACACAAT
7268288 ACTAAACCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.02
23 45 0.96
24 1 0.02
ACGTcount: A:0.40, C:0.33, G:0.08, T:0.19
Consensus pattern (23 bp):
TCACACAATGACATATCAACCAC
Found at i:7271859 original size:17 final size:15
Alignment explanation
Indices: 7271833--7271867 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
7271823 ATAATTTTTT
7271833 AATTTTTAAAAATTAA
1 AATTTTTAAAAA-TAA
7271849 AATTATTTAAAAATAA
1 AATT-TTTAAAAATAA
7271865 AAT
1 AAT
7271868 CCACATAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTTTTAAAAATAA
Found at i:7276363 original size:20 final size:20
Alignment explanation
Indices: 7276338--7276375 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
7276328 TCTGACATTA
*
7276338 AAACAAATAAGGATAAGGTT
1 AAACAAATAAGGACAAGGTT
7276358 AAACAAATAAGGACAAGG
1 AAACAAATAAGGACAAGG
7276376 ATTGGATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.21, T:0.13
Consensus pattern (20 bp):
AAACAAATAAGGACAAGGTT
Found at i:7284560 original size:18 final size:21
Alignment explanation
Indices: 7284539--7284580 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 21
7284529 AAAATGATAG
7284539 AAATATGTAA-AA-TAA-AAT
1 AAATATGTAATAATTAAGAAT
*
7284557 AAATTTGTAATAATTAAGAAT
1 AAATATGTAATAATTAAGAAT
7284578 AAA
1 AAA
7284581 AATAAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 3 0.15
21 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (21 bp):
AAATATGTAATAATTAAGAAT
Found at i:7290214 original size:16 final size:17
Alignment explanation
Indices: 7290189--7290231 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
7290179 TTATTTTGTG
7290189 TTAATGTTATAAAAATTA
1 TTAAT-TTATAAAAATTA
7290207 -TAATTTAT-AAAATTA
1 TTAATTTATAAAAATTA
7290222 TTAA-TTATAA
1 TTAATTTATAA
7290232 TATACATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 11 0.48
16 8 0.35
17 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TTAATTTATAAAAATTA
Found at i:7316331 original size:32 final size:32
Alignment explanation
Indices: 7316290--7316370 Score: 153
Period size: 32 Copynumber: 2.5 Consensus size: 32
7316280 GCAGGCACCC
7316290 AGTAACCAAATGATGTTTCTTTTTTGAAAGGA
1 AGTAACCAAATGATGTTTCTTTTTTGAAAGGA
*
7316322 AGTAACCAAATGATGTTTCTTTTTTGCAAGGA
1 AGTAACCAAATGATGTTTCTTTTTTGAAAGGA
7316354 AGTAACCAAATGATGTT
1 AGTAACCAAATGATGTT
7316371 ATTATGGTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.36
Consensus pattern (32 bp):
AGTAACCAAATGATGTTTCTTTTTTGAAAGGA
Found at i:7332253 original size:13 final size:13
Alignment explanation
Indices: 7332237--7332277 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
7332227 CTTTCATTCT
7332237 CTCCTTTTCTCTC
1 CTCCTTTTCTCTC
7332250 CTCC-TTTCTCTC
1 CTCCTTTTCTCTC
*
7332262 CTATCTTTTCT-TC
1 CT-CCTTTTCTCTC
7332275 CTC
1 CTC
7332278 GTAGCCCGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 10 0.42
13 9 0.38
14 5 0.21
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (13 bp):
CTCCTTTTCTCTC
Found at i:7336851 original size:2 final size:2
Alignment explanation
Indices: 7336844--7336876 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7336834 GAAATGTATG
7336844 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7336877 TAATTAGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7354844 original size:2 final size:2
Alignment explanation
Indices: 7354821--7354867 Score: 62
Period size: 2 Copynumber: 24.0 Consensus size: 2
7354811 TATGGTATGG
*
7354821 TA TA -A TA TA CA TA TA TCA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
7354862 TA TA TA
1 TA TA TA
7354868 GAGAGAGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 37 0.93
3 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:7354872 original size:2 final size:2
Alignment explanation
Indices: 7354867--7354892 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7354857 ATATATATAT
7354867 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
7354893 GGGCTTCACA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7362859 original size:6 final size:6
Alignment explanation
Indices: 7362850--7362880 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
7362840 ATGGAGAGGG
7362850 AGCAAC AGCAAC AGCAAC AGCAAC AGCAAC A
1 AGCAAC AGCAAC AGCAAC AGCAAC AGCAAC A
7362881 ACAGCAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.32, G:0.16, T:0.00
Consensus pattern (6 bp):
AGCAAC
Found at i:7373215 original size:3 final size:3
Alignment explanation
Indices: 7373207--7373232 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7373197 TTTCTTTTAC
7373207 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
7373233 GCCTCTTCAG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:7383194 original size:2 final size:2
Alignment explanation
Indices: 7383187--7383220 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
7383177 TGCTCAAGCA
7383187 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
7383221 GTATCCTAAT
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:7385437 original size:28 final size:29
Alignment explanation
Indices: 7385404--7385458 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
7385394 ATTTAAAAAT
7385404 ATTTAAATAAGTCTTTAT-TTTTTATTAC
1 ATTTAAATAAGTCTTTATATTTTTATTAC
* *
7385432 ATTTAATTAAGTTTTTATATTTTTATT
1 ATTTAAATAAGTCTTTATATTTTTATT
7385459 TTGAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 16 0.67
29 8 0.33
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (29 bp):
ATTTAAATAAGTCTTTATATTTTTATTAC
Found at i:7385455 original size:30 final size:30
Alignment explanation
Indices: 7385406--7385480 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 30
7385396 TTAAAAATAT
* ** *
7385406 TTAAATAAGTCTTTAT-TTTTTAT-TACAT
1 TTAAATAAGTTTTTATATTTTTATATTGAA
* *
7385434 TTAATTAAGTTTTTATATTTTTATTTTGAA
1 TTAAATAAGTTTTTATATTTTTATATTGAA
7385464 TTAAATAAGTTTTTATA
1 TTAAATAAGTTTTTATA
7385481 ATTAATGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 14 0.36
29 7 0.18
30 18 0.46
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (30 bp):
TTAAATAAGTTTTTATATTTTTATATTGAA
Found at i:7388901 original size:2 final size:2
Alignment explanation
Indices: 7388894--7388922 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7388884 ATTTATTTAC
7388894 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7388923 GTAGAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7390341 original size:17 final size:17
Alignment explanation
Indices: 7390311--7390343 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
7390301 CTTTTTTTTT
7390311 TTTTGTGTTAACGTGTG
1 TTTTGTGTTAACGTGTG
7390328 TTTTG-GTTACACGTGT
1 TTTTGTGTTA-ACGTGT
7390344 CAATTTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.12, C:0.09, G:0.27, T:0.52
Consensus pattern (17 bp):
TTTTGTGTTAACGTGTG
Found at i:7395631 original size:2 final size:2
Alignment explanation
Indices: 7395624--7395656 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7395614 AAGGATTTAA
7395624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7395657 CATGTATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7398550 original size:2 final size:2
Alignment explanation
Indices: 7398531--7398567 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
7398521 TACAAATTTA
* *
7398531 AT AT AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7398568 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:7400176 original size:2 final size:2
Alignment explanation
Indices: 7400169--7400211 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
7400159 ATGGCGCTTC
*
7400169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7400210 AT
1 AT
7400212 TCCCAGGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:7401543 original size:9 final size:9
Alignment explanation
Indices: 7401523--7401582 Score: 86
Period size: 9 Copynumber: 6.4 Consensus size: 9
7401513 GAGGCAAAGT
7401523 TTTTATTTTA
1 TTTTA-TTTA
7401533 TTTTATTTA
1 TTTTATTTA
7401542 TTTTATTTA
1 TTTTATTTA
7401551 TTTTATTTA
1 TTTTATTTA
7401560 TTATTA-TTA
1 TT-TTATTTA
7401569 TTTATATTTA
1 TTT-TATTTA
7401579 TTTT
1 TTTT
7401583 TTTTTCAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
8 1 0.02
9 32 0.68
10 14 0.30
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTATTTA
Found at i:7401552 original size:13 final size:13
Alignment explanation
Indices: 7401524--7401585 Score: 58
Period size: 13 Copynumber: 4.6 Consensus size: 13
7401514 AGGCAAAGTT
7401524 TTTATTTTATTTTA
1 TTTATTTTA-TTTA
7401538 TTTATTTTATTTA
1 TTTATTTTATTTA
7401551 TTT-TATTTA-TTA
1 TTTAT-TTTATTTA
7401563 TTATTATTTATATTTA
1 -T-TTATTT-TATTTA
7401579 TTT-TTTT
1 TTTATTTT
7401586 TTCAATTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
12 5 0.12
13 15 0.36
14 15 0.36
15 4 0.10
16 3 0.07
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:7401558 original size:28 final size:29
Alignment explanation
Indices: 7401523--7401587 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
7401513 GAGGCAAAGT
7401523 TTTTATTTTATT-TTATTTATTT-TATTTA
1 TTTTATTTTATTATTA-TTATTTATATTTA
7401551 TTTTA-TTTATTATTATTATTTATATTTA
1 TTTTATTTTATTATTATTATTTATATTTA
*
7401579 TTTTTTTTT
1 TTTTATTTT
7401588 CAATTCTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 12 0.36
28 18 0.55
29 3 0.09
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTTATTTTATTATTATTATTTATATTTA
Found at i:7418952 original size:29 final size:28
Alignment explanation
Indices: 7418920--7418977 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
7418910 ACGAAGATCC
* * *
7418920 GCAATGGCATTTGTGTCTCTTAAGTGTAT
1 GCAAAGGCATTTGTCTC-CCTAAGTGTAT
7418949 GCAAAGGCATTTGTCTCCCTAAGTGTAT
1 GCAAAGGCATTTGTCTCCCTAAGTGTAT
7418977 G
1 G
7418978 ACGTAGCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.36
Consensus pattern (28 bp):
GCAAAGGCATTTGTCTCCCTAAGTGTAT
Found at i:7419361 original size:2 final size:2
Alignment explanation
Indices: 7419354--7419388 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
7419344 ATTAATATTT
7419354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7419389 AGAGTCTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7429197 original size:16 final size:18
Alignment explanation
Indices: 7429168--7429200 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
7429158 TTAGATTCGA
7429168 TTTTATTGATATTTTATT
1 TTTTATTGATATTTTATT
7429186 TTTTATT-A-ATTTTAT
1 TTTTATTGATATTTTAT
7429201 AAAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (18 bp):
TTTTATTGATATTTTATT
Found at i:7429398 original size:21 final size:21
Alignment explanation
Indices: 7429356--7429400 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
7429346 GAAATTTTAA
*
7429356 AAATTATTTTTAATTATTATT
1 AAATTATTTTTAATTATAATT
*
7429377 AAATTAATTTTTTATTA-AATT
1 AAATT-ATTTTTAATTATAATT
7429398 AAA
1 AAA
7429401 CTATAAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAATTATTTTTAATTATAATT
Found at i:7435503 original size:17 final size:15
Alignment explanation
Indices: 7435443--7435504 Score: 56
Period size: 17 Copynumber: 3.9 Consensus size: 15
7435433 GAGTAAAAGT
7435443 AAAA-AATAGAAATAA
1 AAAATAATA-AAATAA
7435458 AAAATAATTAATAATAA
1 AAAATAA-TAA-AATAA
*
7435475 TAAAT-ATAAAATAA
1 AAAATAATAAAATAA
7435489 AAAGATAATAGAAATA
1 AAA-ATAATA-AAATA
7435505 TATGTAGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 7 0.18
15 9 0.23
16 7 0.18
17 16 0.41
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (15 bp):
AAAATAATAAAATAA
Found at i:7442589 original size:2 final size:2
Alignment explanation
Indices: 7442582--7442612 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7442572 TGAAAGAAAT
7442582 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7442613 TGTGGTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7445869 original size:2 final size:2
Alignment explanation
Indices: 7445862--7445892 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7445852 TATTATCTTT
7445862 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7445893 TGAAAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7456859 original size:2 final size:2
Alignment explanation
Indices: 7456852--7456911 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
7456842 TAATTAGCAC
7456852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7456894 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
7456912 CATTTAACTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7461282 original size:2 final size:2
Alignment explanation
Indices: 7461275--7461300 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7461265 TCAATTTTGG
7461275 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
7461301 CGATATCCAA
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:7486130 original size:56 final size:56
Alignment explanation
Indices: 7486068--7486183 Score: 196
Period size: 56 Copynumber: 2.1 Consensus size: 56
7486058 TTGACTATCG
* *
7486068 ACTCAGTCTATAATATTATGGTAAAGAGTTAGTATTTGATTGAATTAGTCTATCAA
1 ACTCAGTCTATAATATCATGGTAAAGAGTTAGTATTTCATTGAATTAGTCTATCAA
* *
7486124 ACTCAGTCTATAATATCGTGGTAAAGAGTTAGTCTTTCATTGAATTAGTCTATCAA
1 ACTCAGTCTATAATATCATGGTAAAGAGTTAGTATTTCATTGAATTAGTCTATCAA
7486180 ACTC
1 ACTC
7486184 TTTGATTGAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (56 bp):
ACTCAGTCTATAATATCATGGTAAAGAGTTAGTATTTCATTGAATTAGTCTATCAA
Found at i:7486222 original size:82 final size:82
Alignment explanation
Indices: 7486102--7486265 Score: 247
Period size: 82 Copynumber: 2.0 Consensus size: 82
7486092 AGAGTTAGTA
* *
7486102 TTTGATTGAATTAGTCTATCAAACTCAGTCTATAATATCGTGGTAAAGAGTTAGTCTTTCATTGA
1 TTTGATTGAATCAATCTATCAAACTCAGTCTATAATATCGTGGTAAAGAGTTAGTCTTTCATTGA
*
7486167 ATTAGTCTATCAAACTC
66 ATCAGTCTATCAAACTC
* * * * *
7486184 TTTGATTGAATCAATCTATTAGACTTAGTTTATAATATCGTGGTAAAGAGTTAGTCTTTGATTGA
1 TTTGATTGAATCAATCTATCAAACTCAGTCTATAATATCGTGGTAAAGAGTTAGTCTTTCATTGA
*
7486249 ATCATTCTATCAAACTC
66 ATCAGTCTATCAAACTC
7486266 AATCTTTTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (82 bp):
TTTGATTGAATCAATCTATCAAACTCAGTCTATAATATCGTGGTAAAGAGTTAGTCTTTCATTGA
ATCAGTCTATCAAACTC
Found at i:7488080 original size:43 final size:43
Alignment explanation
Indices: 7488019--7488103 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 43
7488009 ATTGCAACAG
* *
7488019 TCTAATTTAATGAAGCAAAGTGAAATGATATATCATTAATTAT
1 TCTAATCTAAAGAAGCAAAGTGAAATGATATATCATTAATTAT
*
7488062 TCTAATCTAAAGAAGCAAAGTGGAATGATATATCATTAATTA
1 TCTAATCTAAAGAAGCAAAGTGAAATGATATATCATTAATTA
7488104 GCATTAAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (43 bp):
TCTAATCTAAAGAAGCAAAGTGAAATGATATATCATTAATTAT
Found at i:7489778 original size:2 final size:2
Alignment explanation
Indices: 7489771--7489795 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7489761 ATGATTTGAC
7489771 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
7489796 GTTAATGCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7498264 original size:13 final size:14
Alignment explanation
Indices: 7498246--7498275 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
7498236 TGTACCTTTA
7498246 TTTCCGGTTGTC-C
1 TTTCCGGTTGTCGC
7498259 TTTCCGGTTGTCGC
1 TTTCCGGTTGTCGC
7498273 TTT
1 TTT
7498276 TGATTTATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.00, C:0.27, G:0.23, T:0.50
Consensus pattern (14 bp):
TTTCCGGTTGTCGC
Found at i:7503939 original size:100 final size:101
Alignment explanation
Indices: 7503761--7503961 Score: 350
Period size: 100 Copynumber: 2.0 Consensus size: 101
7503751 ACTTTCTGCT
*
7503761 AATATATGCATTTCTGATTGATCTGTATGGTTTAATAGAGTTGGAATGTTGGGGCCTCTGGATCT
1 AATATATGCATTTCTGATTGATCTGTATGGTTTAATAGAGTTGGAATGTTGGGGCCTCTGGATCC
*
7503826 TGTGAATCAAAGTC-TTCTCATGTAATCTCAGCAAC
66 TGTGAATCAAAGTCTTTCTCATGTAAACTCAGCAAC
*
7503861 AATATATGCATTTCTGATTGATCTGTATGGTTTAATAGAGTTGGAATGTTGGTGCCTCTGGATCC
1 AATATATGCATTTCTGATTGATCTGTATGGTTTAATAGAGTTGGAATGTTGGGGCCTCTGGATCC
* *
7503926 TGTGAATCCAAGTCTTTCTCATGTAAACTTAGCAAC
66 TGTGAATCAAAGTCTTTCTCATGTAAACTCAGCAAC
7503962 GATAGGCAAA
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 76 0.80
101 19 0.20
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.37
Consensus pattern (101 bp):
AATATATGCATTTCTGATTGATCTGTATGGTTTAATAGAGTTGGAATGTTGGGGCCTCTGGATCC
TGTGAATCAAAGTCTTTCTCATGTAAACTCAGCAAC
Found at i:7513764 original size:2 final size:2
Alignment explanation
Indices: 7513747--7513787 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
7513737 GTTTGATGGT
* *
7513747 TA TA GA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7513788 TCAGAATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:7516024 original size:2 final size:2
Alignment explanation
Indices: 7516017--7516045 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7516007 GTGAATATGA
7516017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7516046 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7517654 original size:19 final size:20
Alignment explanation
Indices: 7517612--7517654 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
7517602 TTTTTTTTTC
*
7517612 TTTTGAATTTCATCTTAGAA
1 TTTTGAATTTCATCCTAGAA
7517632 -TTTGAATTTCATCCTA-AA
1 TTTTGAATTTCATCCTAGAA
7517650 TTTTG
1 TTTTG
7517655 TTCCTGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (20 bp):
TTTTGAATTTCATCCTAGAA
Found at i:7517774 original size:27 final size:27
Alignment explanation
Indices: 7517738--7517812 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
7517728 ATATTGAATA
* *
7517738 TTGGTTTTGTTCTGTAGATTGTTTAG-
1 TTGGTATTGTTATGTAGATTGTTTAGT
*
7517764 TTGGATATTGTTTTGTAGATTGTTTAGT
1 TTGG-TATTGTTATGTAGATTGTTTAGT
7517792 TTGGTATTGTTATGTAGATTG
1 TTGGTATTGTTATGTAGATTG
7517813 GCTTGAATGA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.09
27 36 0.82
28 4 0.09
ACGTcount: A:0.16, C:0.01, G:0.27, T:0.56
Consensus pattern (27 bp):
TTGGTATTGTTATGTAGATTGTTTAGT
Found at i:7522197 original size:12 final size:12
Alignment explanation
Indices: 7522155--7522196 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
7522145 TAACCATGCT
7522155 ATTTCTAAT-AA
1 ATTTCTAATGAA
*
7522166 AATTCTAATGAA
1 ATTTCTAATGAA
*
7522178 ATTTTCTGATGAA
1 A-TTTCTAATGAA
7522191 ATTTCT
1 ATTTCT
7522197 GTTGACATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 8 0.31
12 8 0.31
13 10 0.38
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (12 bp):
ATTTCTAATGAA
Found at i:7541519 original size:16 final size:15
Alignment explanation
Indices: 7541498--7541541 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
7541488 TGTGACGTCA
*
7541498 AATATATATATGCAT
1 AATATATATATACAT
*
7541513 GAATATATGTATACAT
1 -AATATATATATACAT
7541529 ATATATATATATA
1 A-ATATATATATA
7541542 TATATTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (15 bp):
AATATATATATACAT
Found at i:7544886 original size:21 final size:21
Alignment explanation
Indices: 7544860--7544912 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
7544850 TGATGAATGA
*
7544860 AGTATCGATACTCAATAAACT
1 AGTATCGATACTCAATAAACC
* *
7544881 AGTATCAATACTCGATAAACC
1 AGTATCGATACTCAATAAACC
7544902 AGTATCGATAC
1 AGTATCGATAC
7544913 CATTACCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (21 bp):
AGTATCGATACTCAATAAACC
Found at i:7546279 original size:41 final size:41
Alignment explanation
Indices: 7546164--7546281 Score: 112
Period size: 41 Copynumber: 2.9 Consensus size: 41
7546154 GACACCTTTG
* *
7546164 TATGTTCCAAGTAGTGAGGATGAT-ACCTTACCCTCTTATTGA
1 TATGTTCCAAGTAGCGAGGATGATAACC-TACCCT-TCATTGA
* * * * * * * *
7546206 TATATTTCAAGTGGCGGGGACGATATCGTACCCTTCATTTA
1 TATGTTCCAAGTAGCGAGGATGATAACCTACCCTTCATTGA
*
7546247 TATGTTCCAAGTAGCAAGGATGATAACCTACCCTT
1 TATGTTCCAAGTAGCGAGGATGATAACCTACCCTT
7546282 TGTATAAAAT
Statistics
Matches: 57, Mismatches: 18, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
41 32 0.56
42 24 0.42
43 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
TATGTTCCAAGTAGCGAGGATGATAACCTACCCTTCATTGA
Found at i:7546847 original size:21 final size:21
Alignment explanation
Indices: 7546823--7546878 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
7546813 ATTTTGTGTT
*
7546823 AAAAGCATCAATACTTATGAC
1 AAAAGTATCAATACTTATGAC
7546844 AAAAGTATCAATACTTATGAC
1 AAAAGTATCAATACTTATGAC
7546865 AAAAGTATCAATAC
1 AAAAGTATCAATAC
7546879 CTTGAGCCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.25
Consensus pattern (21 bp):
AAAAGTATCAATACTTATGAC
Found at i:7551706 original size:14 final size:14
Alignment explanation
Indices: 7551683--7551715 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7551673 AGAAAATACG
7551683 ATAT-AATATAAAA
1 ATATAAATATAAAA
*
7551696 TTATAAATATAAAA
1 ATATAAATATAAAA
7551710 ATATAA
1 ATATAA
7551716 TGGTTGTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATATAAATATAAAA
Found at i:7566003 original size:37 final size:37
Alignment explanation
Indices: 7565962--7566032 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
7565952 TGTTGCTTTA
*
7565962 TTGTCACAATGTATCAAGATTGGTGTCATTAGTTTTG
1 TTGTCACAATGTATCAAGATTGGTGCCATTAGTTTTG
7565999 TTGTCACAATGTATCAAGATTGGTGCCATTAGTT
1 TTGTCACAATGTATCAAGATTGGTGCCATTAGTT
7566033 GAAGCCATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (37 bp):
TTGTCACAATGTATCAAGATTGGTGCCATTAGTTTTG
Found at i:7573811 original size:21 final size:21
Alignment explanation
Indices: 7573785--7573837 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
7573775 TGTTCATACA
*
7573785 ATTCATGACAAAGGCTAATGC
1 ATTCATGACAAAGACTAATGC
* * *
7573806 ATTCATAACAAAGATTGATGC
1 ATTCATGACAAAGACTAATGC
*
7573827 ATTTATGACAA
1 ATTCATGACAA
7573838 GGATTGATAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (21 bp):
ATTCATGACAAAGACTAATGC
Found at i:7573842 original size:21 final size:21
Alignment explanation
Indices: 7573802--7573845 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7573792 ACAAAGGCTA
7573802 ATGCATTCATAACAAAGATTG
1 ATGCATTCATAACAAAGATTG
* * *
7573823 ATGCATTTATGACAAGGATTG
1 ATGCATTCATAACAAAGATTG
7573844 AT
1 AT
7573846 ACCTCCATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (21 bp):
ATGCATTCATAACAAAGATTG
Found at i:7578741 original size:35 final size:34
Alignment explanation
Indices: 7578644--7578743 Score: 121
Period size: 35 Copynumber: 2.9 Consensus size: 34
7578634 TCTTATATTG
*
7578644 AAATAAAAGGAAAGTCATGTATGTTGGAAATTAAA
1 AAATAAAA-GAAAGTCATGTTTGTTGGAAATTAAA
* *
7578679 AAATAAAAGAAAGGTCACGTTTTTTGGAAA-TAGAA
1 AAATAAAAGAAA-GTCATGTTTGTTGGAAATTA-AA
*
7578714 AAATAAAAGAAGAGTCATATTTGTTGGAAA
1 AAATAAAAGAA-AGTCATGTTTGTTGGAAA
7578744 AAACCAACTG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.11
35 49 0.88
36 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.26
Consensus pattern (34 bp):
AAATAAAAGAAAGTCATGTTTGTTGGAAATTAAA
Found at i:7579370 original size:33 final size:30
Alignment explanation
Indices: 7579294--7579371 Score: 86
Period size: 33 Copynumber: 2.5 Consensus size: 30
7579284 ATGTTACAGC
7579294 ATTATAAAAATAAAT-TTAAAATTTTTAAAG
1 ATTA-AAAAATAAATATTAAAATTTTTAAAG
* * *
7579324 ATTTAAAATTAAATATTAATAATTTTTTAAG
1 ATTAAAAAATAAATATTAA-AATTTTTAAAG
7579355 AATATAAAAAATAAATA
1 -AT-TAAAAAATAAATA
7579372 CAATTTTCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 9 0.23
30 7 0.18
31 10 0.26
32 2 0.05
33 11 0.28
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.40
Consensus pattern (30 bp):
ATTAAAAAATAAATATTAAAATTTTTAAAG
Found at i:7590277 original size:37 final size:37
Alignment explanation
Indices: 7590235--7590306 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
7590225 TAGTAAGATT
*
7590235 AAAGGTTATGTCCAAAGACAAAAAGGTACTTCAATTG
1 AAAGGTTATGTCCAAAGACAAAAAGGCACTTCAATTG
* * *
7590272 AAAGGTTGTGTCTAAAGACAAATAGGCACTTCAAT
1 AAAGGTTATGTCCAAAGACAAAAAGGCACTTCAAT
7590307 GTAAAGTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (37 bp):
AAAGGTTATGTCCAAAGACAAAAAGGCACTTCAATTG
Found at i:7591030 original size:15 final size:16
Alignment explanation
Indices: 7591012--7591044 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
7591002 CTTATTTGGA
7591012 TTTTGTTA-CTTTTAT
1 TTTTGTTATCTTTTAT
*
7591027 TTTTGTTATTTTTTAT
1 TTTTGTTATCTTTTAT
7591043 TT
1 TT
7591045 CACTTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.12, C:0.03, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTGTTATCTTTTAT
Found at i:7593030 original size:80 final size:80
Alignment explanation
Indices: 7592880--7593030 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 80
7592870 AAAAAAAATC
* * ** * *
7592880 AAATTCTTCTCTTCTCTTCCCTAGAATTTGTAAAAGAAATCTGATGCTCTTCTCTTCTTTAGAAT
1 AAATTCTTCTCTTCTCTTCCCTAGAATCTATAAAAGAAATCCAATGCTCTTCTCTTCTCTAAAAT
*
7592945 TTATAAAAGAAAGTT
66 CTATAAAAGAAAGTT
* * * * *
7592960 AAATTCTTCTCTTCTCTTCCCTATAATCTATATAGGACATCCAATGCTCTTTTCTTCTCTAAAAT
1 AAATTCTTCTCTTCTCTTCCCTAGAATCTATAAAAGAAATCCAATGCTCTTCTCTTCTCTAAAAT
7593025 CTATAA
66 CTATAA
7593031 GGGAAATATG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
80 59 1.00
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (80 bp):
AAATTCTTCTCTTCTCTTCCCTAGAATCTATAAAAGAAATCCAATGCTCTTCTCTTCTCTAAAAT
CTATAAAAGAAAGTT
Found at i:7594838 original size:32 final size:32
Alignment explanation
Indices: 7594797--7594858 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
7594787 GTGGCTCGTG
*
7594797 ACACATGCATG-CTCCGAGTTGATTGAGTTTCT
1 ACACATGCATGCCT-CGAGTTGAATGAGTTTCT
7594829 ACACATGCATGCCTCGAGTTGAATGAGTTT
1 ACACATGCATGCCTCGAGTTGAATGAGTTT
7594859 TTAAACAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (32 bp):
ACACATGCATGCCTCGAGTTGAATGAGTTTCT
Found at i:7597546 original size:16 final size:17
Alignment explanation
Indices: 7597521--7597558 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
7597511 GATTTCATAC
*
7597521 AATAGTTAAAT-ATATA
1 AATAGGTAAATAATATA
7597537 AATAGGTAAATAATATA
1 AATAGGTAAATAATATA
7597554 AATAG
1 AATAG
7597559 AAAAAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32
Consensus pattern (17 bp):
AATAGGTAAATAATATA
Found at i:7597660 original size:32 final size:31
Alignment explanation
Indices: 7597607--7597669 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
7597597 GTTACTAGAA
*
7597607 AAGAGAAAAAAAAATAAAAAGACACGAAAGAG
1 AAGAGAAAAAAAAAGAAAAAGACA-GAAAGAG
* * *
7597639 AAGAGAAAAAGAAAGAGAAAGAGAGAAAGAG
1 AAGAGAAAAAAAAAGAAAAAGACAGAAAGAG
7597670 GTGTGGAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.70, C:0.03, G:0.25, T:0.02
Consensus pattern (31 bp):
AAGAGAAAAAAAAAGAAAAAGACAGAAAGAG
Found at i:7597662 original size:18 final size:17
Alignment explanation
Indices: 7597632--7597668 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
7597622 AAAAAGACAC
7597632 GAAAGAGAAGAGAAAAA
1 GAAAGAGAAGAGAAAAA
*
7597649 GAAAGAGAAAGAGAGAAA
1 GAAAGAG-AAGAGAAAAA
7597667 GA
1 GA
7597669 GGTGTGGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
GAAAGAGAAGAGAAAAA
Found at i:7597826 original size:48 final size:56
Alignment explanation
Indices: 7597761--7597884 Score: 158
Period size: 48 Copynumber: 2.3 Consensus size: 56
7597751 TAAAAAAATT
*
7597761 ATTTTGAGGGGATCATTAAAA-ATATATA-ATA-A-ATAAA-TA-A-ATTTT-AAA
1 ATTTTGAGGGGACCATTAAAATATATATATATATATATAAATTACATATTTTAAAA
7597809 ATTTTGAGGGGACCATTAAAATATATATATATATATATAAATTACATATTTTCAAAA
1 ATTTTGAGGGGACCATTAAAATATATATATATATATATAAATTACATATTTT-AAAA
7597866 ATTTTG-GGGGACCAATTAA
1 ATTTTGAGGGGACC-ATTAA
7597885 TGGCTTACCG
Statistics
Matches: 65, Mismatches: 1, Indels: 11
0.84 0.01 0.14
Matches are distributed among these distances:
48 20 0.31
49 7 0.11
50 3 0.05
51 1 0.02
52 5 0.08
53 2 0.03
54 1 0.02
55 5 0.08
56 7 0.11
57 14 0.22
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (56 bp):
ATTTTGAGGGGACCATTAAAATATATATATATATATATAAATTACATATTTTAAAA
Found at i:7606951 original size:28 final size:29
Alignment explanation
Indices: 7606911--7606965 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
7606901 TTTGTTCCAA
*
7606911 AATAAAAGTATAAAGACTTA-TTGAATGC
1 AATAAAAGAATAAAGACTTATTTGAATGC
*
7606939 AATAAAAGAATAAAGAGTTATTTGAAT
1 AATAAAAGAATAAAGACTTATTTGAAT
7606966 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.29
Consensus pattern (29 bp):
AATAAAAGAATAAAGACTTATTTGAATGC
Found at i:7621041 original size:25 final size:26
Alignment explanation
Indices: 7621013--7621070 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 26
7621003 AATATCAAAT
7621013 TAATATATCA-TATCATCA-TCAATTA
1 TAATATATCAGTAT-ATCAGTCAATTA
*
7621038 TAATACATCAGTATATCATGTCAATTA
1 TAATATATCAGTATATCA-GTCAATTA
7621065 TAATAT
1 TAATAT
7621071 TTTAACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 13 0.46
26 3 0.11
27 12 0.43
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (26 bp):
TAATATATCAGTATATCAGTCAATTA
Found at i:7627055 original size:27 final size:27
Alignment explanation
Indices: 7627016--7627074 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
7627006 GGTTTCAATA
*
7627016 TTGCTTCATTATTCCTTAGGCTGTGTG
1 TTGCTTCACTATTCCTTAGGCTGTGTG
7627043 TTGCTTCACTATTCCTTAGGCTGTGTG
1 TTGCTTCACTATTCCTTAGGCTGTGTG
7627070 TTGCT
1 TTGCT
7627075 GTAAAGAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.10, C:0.20, G:0.22, T:0.47
Consensus pattern (27 bp):
TTGCTTCACTATTCCTTAGGCTGTGTG
Found at i:7634429 original size:25 final size:24
Alignment explanation
Indices: 7634392--7634438 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
7634382 TCTTGTTCTT
*
7634392 CCTTCCTTTTTCTCCTTCTTCTCA
1 CCTTCCTTCTTCTCCTTCTTCTCA
*
7634416 CCTTGCCTTCTTCTCTTTCTTCT
1 CCTT-CCTTCTTCTCCTTCTTCT
7634439 TACTATCCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.02, C:0.40, G:0.02, T:0.55
Consensus pattern (24 bp):
CCTTCCTTCTTCTCCTTCTTCTCA
Found at i:7635080 original size:15 final size:17
Alignment explanation
Indices: 7635050--7635090 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
7635040 TTACAATGTA
7635050 ATTTTCTCAGCAATCAC
1 ATTTTCTCAGCAATCAC
7635067 ATTTTCT-A-CAATCATC
1 ATTTTCTCAGCAATCA-C
*
7635083 ACTTTCTC
1 ATTTTCTC
7635091 TATTACACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.29
16 8 0.38
17 7 0.33
ACGTcount: A:0.27, C:0.29, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTTTCTCAGCAATCAC
Found at i:7635177 original size:15 final size:15
Alignment explanation
Indices: 7635117--7635180 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
7635107 GTAAGGTTCT
*
7635117 ATTCTCAATAATTAC
1 ATTCTCAATAATCAC
* ** *
7635132 ATTCCCAGCAATCAT
1 ATTCTCAATAATCAC
* *
7635147 ATACTCAATAACCAC
1 ATTCTCAATAATCAC
*
7635162 ATTCTCAGTAATCAC
1 ATTCTCAATAATCAC
7635177 ATTC
1 ATTC
7635181 CCAACAATAT
Statistics
Matches: 35, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (15 bp):
ATTCTCAATAATCAC
Found at i:7635272 original size:22 final size:20
Alignment explanation
Indices: 7635247--7635288 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
7635237 CATTAGTTTA
7635247 ATAATGTATTAATATTTTTATT
1 ATAATGTA-TAAT-TTTTTATT
*
7635269 ATAATTTATAATTTTTTATT
1 ATAATGTATAATTTTTTATT
7635289 TTTAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATAATGTATAATTTTTTATT
Found at i:7635298 original size:15 final size:16
Alignment explanation
Indices: 7635273--7635306 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
7635263 TTTATTATAA
*
7635273 TTTATAATTTTTTATT
1 TTTATAATTTTTAATT
7635289 TTTA-AATTTTTAATT
1 TTTATAATTTTTAATT
7635304 TTT
1 TTT
7635307 TCTCTCTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATAATTTTTAATT
Found at i:7635302 original size:22 final size:20
Alignment explanation
Indices: 7635255--7635307 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
7635245 TAATAATGTA
7635255 TTAATATTTTTATTATAATTT
1 TTAAT-TTTTTATTATAATTT
* *
7635276 ATAATTTTTTATTTTTAAATTT
1 TTAATTTTTTA-TTAT-AATTT
7635298 TTAATTTTTT
1 TTAATTTTTT
7635308 CTCTCTCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.22
21 7 0.26
22 14 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTAATTTTTTATTATAATTT
Found at i:7646341 original size:7 final size:7
Alignment explanation
Indices: 7646316--7646354 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
7646306 TTTTGTACAT
7646316 AGAAAAA
1 AGAAAAA
* *
7646323 ATATAAA
1 AGAAAAA
7646330 A-AAAAA
1 AGAAAAA
7646336 AGAAAAA
1 AGAAAAA
7646343 AGAAAAA
1 AGAAAAA
7646350 AGAAA
1 AGAAA
7646355 GAGCAACCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (7 bp):
AGAAAAA
Found at i:7646348 original size:14 final size:14
Alignment explanation
Indices: 7646316--7646354 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
7646306 TTTTGTACAT
* *
7646316 AGAAAAAATATAAA
1 AGAAAAAAGAAAAA
7646330 A-AAAAAAGAAAAA
1 AGAAAAAAGAAAAA
7646343 AGAAAAAAGAAA
1 AGAAAAAAGAAA
7646355 GAGCAACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (14 bp):
AGAAAAAAGAAAAA
Found at i:7652568 original size:99 final size:98
Alignment explanation
Indices: 7652439--7652655 Score: 265
Period size: 99 Copynumber: 2.2 Consensus size: 98
7652429 TAAGCAGGAC
* *
7652439 AAGTAGTAGGGATGTTGCTCCTTTGAGCAGGACAAGTAGCAGGGATGATGCACCTATAAGCACGC
1 AAGTAGTAGGGATGATGC-CCTTTAAGCAGGACAAGTAGCAGGGATGATGCACCTATAAGCACGC
* *
7652504 CAAGTCGT-AGGGATGATGCCCTTATAAGCACTTT
65 CAA-TCATCAGGGATGATGCCCCTATAAGCACTTT
* * * * * *
7652538 AAGTCGTAGGGATGATGCCCTTATAAGCAGGCCAATTATCAGGGATGATGCCCCTATAAGCAGGC
1 AAGTAGTAGGGATGATGCCCTT-TAAGCAGGACAAGTAGCAGGGATGATGCACCTATAAGCACGC
* *
7652603 CAATTATCAGGGATGATGCCCCTATAAGCAGTTT
65 CAATCATCAGGGATGATGCCCCTATAAGCACTTT
* **
7652637 GAGTAACAGGGATGATGCC
1 AAGTAGTAGGGATGATGCC
7652656 TCTATAAACA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
98 6 0.06
99 94 0.94
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (98 bp):
AAGTAGTAGGGATGATGCCCTTTAAGCAGGACAAGTAGCAGGGATGATGCACCTATAAGCACGCC
AATCATCAGGGATGATGCCCCTATAAGCACTTT
Found at i:7652647 original size:33 final size:33
Alignment explanation
Indices: 7652429--7652740 Score: 202
Period size: 33 Copynumber: 9.5 Consensus size: 33
7652419 GACAATCCTT
* * * *
7652429 TAAGCAGGACAAGTAGT-AGGGATGTTGCTCCTT
1 TAAGCAGGCCAAGTA-TCAGGGATGATGCCCCTA
* * * *
7652462 TGAGCAGGACAAGTAGCAGGGATGATGCACCTA
1 TAAGCAGGCCAAGTATCAGGGATGATGCCCCTA
* * *
7652495 TAAGCACGCCAAGTCGT-AGGGATGATGCCCTTA
1 TAAGCAGGCCAAGT-ATCAGGGATGATGCCCCTA
**** * *
7652528 TAAGCACTTTAAGTCGT-AGGGATGATGCCCTTA
1 TAAGCAGGCCAAGT-ATCAGGGATGATGCCCCTA
*
7652561 TAAGCAGGCCAATTATCAGGGATGATGCCCCTA
1 TAAGCAGGCCAAGTATCAGGGATGATGCCCCTA
*
7652594 TAAGCAGGCCAATTATCAGGGATGATGCCCCTA
1 TAAGCAGGCCAAGTATCAGGGATGATGCCCCTA
**** * *
7652627 TAAGCAGTTTGAGTAACAGGGATGATGCCTCTA
1 TAAGCAGGCCAAGTATCAGGGATGATGCCCCTA
* ** * * *
7652660 TAAACAGGTTAAGTAGT-GGGGAAGATGCCCCTG
1 TAAGCAGGCCAAGTA-TCAGGGATGATGCCCCTA
** * * * * *
7652693 TAAGTGGGCCAACTA-CTGGAGAAGATTCCCCCA
1 TAAGCAGGCCAAGTATCAGG-GATGATGCCCCTA
7652726 TAAGCAGGCCAAGTA
1 TAAGCAGGCCAAGTA
7652741 GTAAGCATGA
Statistics
Matches: 223, Mismatches: 50, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
32 3 0.01
33 220 0.99
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (33 bp):
TAAGCAGGCCAAGTATCAGGGATGATGCCCCTA
Found at i:7652704 original size:99 final size:99
Alignment explanation
Indices: 7652466--7652696 Score: 234
Period size: 99 Copynumber: 2.3 Consensus size: 99
7652456 CTCCTTTGAG
* * * * * ** *
7652466 CAGGACAAGTAGCAGGGATGATGCACCTATAAGCACGCCAAGTCGT-AGGGATGATGCCCTTATA
1 CAGGCCAAGTATCAGGGAAGATGCCCCTATAAGCAGGCCAA-TTATCAGGGATGATGCCCCTATA
*** *
7652530 AGCACTTTAAGTCGTAGGGATGATGCCCTTATAAG
65 AGCACTTTAAGTAACAGGGATGATGCCCTTATAAA
* *
7652565 CAGGCCAATTATCAGGGATGATGCCCCTATAAGCAGGCCAATTATCAGGGATGATGCCCCTATAA
1 CAGGCCAAGTATCAGGGAAGATGCCCCTATAAGCAGGCCAATTATCAGGGATGATGCCCCTATAA
* *
7652630 GCAGTTTGAGTAACAGGGATGATG-CCTCTATAAA
66 GCACTTTAAGTAACAGGGATGATGCCCT-TATAAA
** * *
7652664 CAGGTTAAGTAGT-GGGGAAGATGCCCCTGTAAG
1 CAGGCCAAGTA-TCAGGGAAGATGCCCCTATAAG
7652697 TGGGCCAACT
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
98 5 0.05
99 103 0.94
100 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (99 bp):
CAGGCCAAGTATCAGGGAAGATGCCCCTATAAGCAGGCCAATTATCAGGGATGATGCCCCTATAA
GCACTTTAAGTAACAGGGATGATGCCCTTATAAA
Found at i:7658117 original size:23 final size:23
Alignment explanation
Indices: 7658091--7658150 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
7658081 AAATTGGTCT
* * *
7658091 ATAGACACGTTTATTGAAACACA
1 ATAGACACATCTATAGAAACACA
*
7658114 ATAGACACATCTATAGAAACACT
1 ATAGACACATCTATAGAAACACA
*
7658137 ATAGACATATCTAT
1 ATAGACACATCTAT
7658151 TGACACAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.27
Consensus pattern (23 bp):
ATAGACACATCTATAGAAACACA
Found at i:7658156 original size:21 final size:22
Alignment explanation
Indices: 7658108--7658158 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
7658098 CGTTTATTGA
7658108 AACACAATAGACACATCTATAG
1 AACACAATAGACACATCTATAG
* * *
7658130 AAACACTATAGACATATCTATTG
1 -AACACAATAGACACATCTATAG
7658153 -ACACAA
1 AACACAA
7658159 CTTTTCGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 5 0.21
23 19 0.79
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.22
Consensus pattern (22 bp):
AACACAATAGACACATCTATAG
Found at i:7661196 original size:13 final size:12
Alignment explanation
Indices: 7661172--7661211 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
7661162 AACCAGCTGG
7661172 AACAAAAAAAAA
1 AACAAAAAAAAA
*
7661184 AGCAAAAATAAAA
1 AACAAAAA-AAAA
7661197 AACAAAAACAAAA
1 AACAAAAA-AAAA
7661210 AA
1 AA
7661212 GGGTAAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.03
Consensus pattern (12 bp):
AACAAAAAAAAA
Found at i:7664261 original size:2 final size:2
Alignment explanation
Indices: 7664254--7664281 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7664244 GAGCACCAAC
7664254 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
7664282 GCATGTTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7670372 original size:11 final size:11
Alignment explanation
Indices: 7670356--7670384 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
7670346 TGTGGGTATG
7670356 CTGAGTGCTTA
1 CTGAGTGCTTA
7670367 CTGAGTGCTTA
1 CTGAGTGCTTA
7670378 CTGAGTG
1 CTGAGTG
7670385 GGTGCTGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.34
Consensus pattern (11 bp):
CTGAGTGCTTA
Found at i:7671861 original size:93 final size:92
Alignment explanation
Indices: 7671702--7671871 Score: 243
Period size: 93 Copynumber: 1.8 Consensus size: 92
7671692 CATTAGTTAC
** *
7671702 ATAACTCAATCTCTCTCAAAACCCTATTGTTGGCTAATTGATATGCATCACTTTACATTAGTTAC
1 ATAACTCAATCTCTCTCAAAACCCTATTGTTAACTAACTGATATGCATCACTTTACATTAGTTAC
7671767 ATTTAACACTTGAAAAATAAAATATATA
66 ATTTAACA-TTGAAAAATAAAATATATA
* ** * *
7671795 ATAACTCAATTTCTCTCAAAACTTTATCT-TTAACTAACTGATTTGCATCACTTTACGTTAGTTA
1 ATAACTCAATCTCTCTCAAAACCCTAT-TGTTAACTAACTGATATGCATCACTTTACATTAGTTA
7671859 CATTTAACATTGA
65 CATTTAACATTGA
7671872 TATCTTTAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
92 4 0.06
93 63 0.93
94 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (92 bp):
ATAACTCAATCTCTCTCAAAACCCTATTGTTAACTAACTGATATGCATCACTTTACATTAGTTAC
ATTTAACATTGAAAAATAAAATATATA
Found at i:7671881 original size:53 final size:53
Alignment explanation
Indices: 7671819--7671924 Score: 144
Period size: 53 Copynumber: 2.0 Consensus size: 53
7671809 CTCAAAACTT
* * *
7671819 TATCTTTAACTAACT-G-ATTTGCATCACTTTACGTTAGTTACATTTAACATTGA
1 TATCTTTAACTAACTAGCA--TGCACCACTTTACATTAGTTACACTTAACATTGA
*
7671872 TATCTTTAACTAGCTAGCATGCACCACTTTACATTAGTTACACTTAACATTGA
1 TATCTTTAACTAACTAGCATGCACCACTTTACATTAGTTACACTTAACATTGA
7671925 AAAATGATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 45 0.96
54 1 0.02
55 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (53 bp):
TATCTTTAACTAACTAGCATGCACCACTTTACATTAGTTACACTTAACATTGA
Found at i:7682794 original size:10 final size:10
Alignment explanation
Indices: 7682781--7682827 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
7682771 CAACACATTT
7682781 TATATTAATA
1 TATATTAATA
7682791 TATATATATATA
1 TATAT-TA-ATA
7682803 TATATT-ATA
1 TATATTAATA
* *
7682812 TGTAATAATA
1 TATATTAATA
7682822 TATATT
1 TATATT
7682828 GTTTTCAACC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 7 0.23
10 12 0.40
11 3 0.10
12 8 0.27
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (10 bp):
TATATTAATA
Found at i:7687667 original size:15 final size:14
Alignment explanation
Indices: 7687646--7687681 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
7687636 TTAAAATATT
*
7687646 TTTTAAAAATTACA
1 TTTTAAAAATTAAA
7687660 TATTTAAAAATTAAA
1 T-TTTAAAAATTAAA
7687675 TTTTAAA
1 TTTTAAA
7687682 GTTTAAGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTTAAAAATTAAA
Found at i:7693473 original size:20 final size:23
Alignment explanation
Indices: 7693434--7693478 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
7693424 TATTTTATTA
7693434 TTTATATTTTATGCATTAT-AGT
1 TTTATATTTTATGCATTATAAGT
*
7693456 TTTATA-TTTA-GTATTATAAGT
1 TTTATATTTTATGCATTATAAGT
7693477 TT
1 TT
7693479 ACATAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 9 0.43
22 6 0.29
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (23 bp):
TTTATATTTTATGCATTATAAGT
Found at i:7710500 original size:2 final size:2
Alignment explanation
Indices: 7710493--7710518 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7710483 ACCAAAAGAA
7710493 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
7710519 CGAATGGTAA
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:7715636 original size:13 final size:13
Alignment explanation
Indices: 7715618--7715643 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7715608 AAAAAAATAT
7715618 ATATATTTACTTA
1 ATATATTTACTTA
7715631 ATATATTTACTTA
1 ATATATTTACTTA
7715644 TTAAAATTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATTTACTTA
Found at i:7717812 original size:31 final size:31
Alignment explanation
Indices: 7717751--7717812 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
7717741 GCATGTGTAG
* * *
7717751 GAAACTCTAAATGATGTGGGACTGACAATTT
1 GAAACCCTAAATGATGTGGGACTAAAAATTT
7717782 GAAACCCTAAATGATGTGGGACTAAAAATTT
1 GAAACCCTAAATGATGTGGGACTAAAAATTT
7717813 AAGTAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (31 bp):
GAAACCCTAAATGATGTGGGACTAAAAATTT
Found at i:7723258 original size:226 final size:226
Alignment explanation
Indices: 7722984--7723650 Score: 823
Period size: 226 Copynumber: 3.0 Consensus size: 226
7722974 ATATAAAATG
* ** * *
7722984 TTATGCATATATATAATTGTATAAATATTATATATATATATATTTAATTTATACATAAATATTAC
1 TTATACATATATATAAAAGTA-ACATATTATATATACATATATTTAATTTATACATAAATATTAC
* * *
7723049 TATAATTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAGTTATTACCTTATA
65 TATAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGA
* * *
7723114 TTTTATAATATA-TATTTATAATTTA-TTATTATTTAATA-TAACTTTGATAT-AAACATT-TAA
130 TTTTATAAAATATTGTTTATAA-TTAGTTATTATTT-ATACAAACTTTGATATAAAACATTATAA
*
7723174 AATATAAGTTATGTCATTAATTCATATATATATA
193 CATATAAGTTATGTCATTAATTCATATATATATA
* * *
7723208 TATATATATATGTATAATACAGTCACATATTATATATACATATATTTAATTTATACATAAATATT
1 T-TATACATATATATAA-A-AGTAACATATTATATATACATATATTTAATTTATACATAAATATT
* * * * *
7723273 ACTACAACTTATAATAGACTTTATTTATATAATTATACTTAATAACTTTATTTGTTATCACCTTA
63 ACTATAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTA
* *
7723338 GATTTTATAAAATATTGTTTATAATTAGTTGTTATTTATACAAACTTTGATATAAAACATTGTAA
128 GATTTTATAAAATATTGTTTATAATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAA
*
7723403 CGTATAA-TT-TG----T-A-TCAT-TA-AT-T-
193 CATATAAGTTATGTCATTAATTCATATATATATA
* * * *
7723425 TTATACATATATATAAAAGTAATATATTATATATACAAATATTTAATTTATACATAAGTATTATT
1 TTATACATATATATAAAAGTAACATATTATATATACATATATTTAATTTATACATAAATATTACT
* * **
7723490 ATAACTTATAATAAAC-TTATTTATATGATTACACTTAATAAGTTTATTAGCTATCATTTTAGAT
66 ATAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGAT
* *
7723554 TTTATAACATATTGTTTATAATTAGTTATTATTTATACAAATTTTGATATAAAACATTATAACAT
131 TTTATAAAATATTGTTTATAATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACAT
* * *
7723619 ATAAGTTATATCATTAATT-TTATATACATA
196 ATAAGTTATGTCATTAATTCATATATATATA
7723649 TT
1 TT
7723651 TATAATTATA
Statistics
Matches: 377, Mismatches: 46, Indels: 40
0.81 0.10 0.09
Matches are distributed among these distances:
213 105 0.28
214 59 0.16
215 2 0.01
216 13 0.03
217 1 0.00
218 1 0.00
219 3 0.01
220 4 0.01
221 7 0.02
222 2 0.01
223 2 0.01
224 3 0.01
225 12 0.03
226 115 0.31
227 31 0.08
228 9 0.02
229 8 0.02
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.47
Consensus pattern (226 bp):
TTATACATATATATAAAAGTAACATATTATATATACATATATTTAATTTATACATAAATATTACT
ATAACTTATAATAAACTTTATTTATATGATTACACTTAATAACTTTATTAGTTATCACCTTAGAT
TTTATAAAATATTGTTTATAATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACAT
ATAAGTTATGTCATTAATTCATATATATATA
Found at i:7725515 original size:20 final size:20
Alignment explanation
Indices: 7725486--7725528 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
7725476 AAAGTGGAGT
*
7725486 AAAAATAAAAGGATAAAAGAG
1 AAAAATAAAAGGA-AAAAAAG
7725507 AAAAA-AAAAGGAAAAAAAG
1 AAAAATAAAAGGAAAAAAAG
7725526 AAA
1 AAA
7725529 GATAGAGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 7 0.33
21 5 0.24
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (20 bp):
AAAAATAAAAGGAAAAAAAG
Found at i:7728556 original size:17 final size:18
Alignment explanation
Indices: 7728510--7728570 Score: 74
Period size: 17 Copynumber: 3.5 Consensus size: 18
7728500 TTTTAAAGTA
*
7728510 ATTT-TATT-TTATTTTCA
1 ATTTATATTATTATTTT-T
7728527 ATTTATATTATTATTTTT
1 ATTTATATTATTATTTTT
7728545 ATTTAT-TTATTATTTTT
1 ATTTATATTATTATTTTT
*
7728562 ATTTCTATT
1 ATTTATATT
7728571 CTATTTACTC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
17 20 0.51
18 12 0.31
19 7 0.18
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTATATTATTATTTTT
Found at i:7728563 original size:23 final size:23
Alignment explanation
Indices: 7728527--7728577 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
7728517 TTTATTTTCA
*
7728527 ATTTATATTATTATTTTTATT-T
1 ATTTATATTATTATTTCTATTCT
*
7728549 ATTTATTATTTTTATTTCTATTCT
1 ATTTA-TATTATTATTTCTATTCT
7728573 ATTTA
1 ATTTA
7728578 CTCATATGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 5 0.20
23 14 0.56
24 6 0.24
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (23 bp):
ATTTATATTATTATTTCTATTCT
Found at i:7728736 original size:15 final size:16
Alignment explanation
Indices: 7728718--7728752 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7728708 TTATTATGTG
*
7728718 AATTTT-ATTTTTAAT
1 AATTTTAATTTTTAAA
7728733 AATTTTAATTTTTAAA
1 AATTTTAATTTTTAAA
7728749 AATT
1 AATT
7728753 AATGATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
AATTTTAATTTTTAAA
Found at i:7739479 original size:2 final size:2
Alignment explanation
Indices: 7739472--7739496 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7739462 TTTAAAGAAC
7739472 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
7739497 AACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7743120 original size:21 final size:21
Alignment explanation
Indices: 7743096--7743155 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
7743086 GGTGTCGACA
*
7743096 TATGCATTTGAGGCTATGCCG
1 TATGCATTTGAGGCCATGCCG
* * *
7743117 TATGCAGTTAAGGCCATGGCG
1 TATGCATTTGAGGCCATGCCG
*
7743138 TATGCATTTGAGGACATG
1 TATGCATTTGAGGCCATG
7743156 GCAGTGTAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (21 bp):
TATGCATTTGAGGCCATGCCG
Found at i:7745660 original size:29 final size:27
Alignment explanation
Indices: 7745546--7745736 Score: 131
Period size: 27 Copynumber: 7.0 Consensus size: 27
7745536 AATAATATAT
* * *
7745546 TTTTTTTCAAAATGACGTGTAACAACC
1 TTTTTTTCAACATGGCGTGTAACAACA
* *
7745573 TTTATTTCAACATGGCGTGTGAA-AATA
1 TTTTTTTCAACATGGCGTGT-AACAACA
* ** *
7745600 TTTTTTTCAAAATTACGTGTAGCAACA
1 TTTTTTTCAACATGGCGTGTAACAACA
* *
7745627 TTTTTTTTATCATGGCGTGTAACAACAA
1 TTTTTTTCAACATGGCGTGTAACAAC-A
*
7745655 TATTTTTTCAACATGGCGTAG-GACAAC-
1 T-TTTTTTCAACATGGCGT-GTAACAACA
* * *
7745682 TTCTTTTCACCATGAG-GTGTAGCTAA-A
1 TTTTTTTCAACATG-GCGTGTAAC-AACA
* *
7745709 TTTTTTTTTAACATGGAGTGTAACAACA
1 -TTTTTTTCAACATGGCGTGTAACAACA
7745737 ACATTTTTCA
Statistics
Matches: 124, Mismatches: 28, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
25 1 0.01
26 15 0.12
27 65 0.52
28 22 0.18
29 20 0.16
30 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (27 bp):
TTTTTTTCAACATGGCGTGTAACAACA
Found at i:7745670 original size:83 final size:83
Alignment explanation
Indices: 7745544--7745744 Score: 205
Period size: 83 Copynumber: 2.4 Consensus size: 83
7745534 ACAATAATAT
* * * * * *
7745544 ATTTTTTTTCAAAATGACGTGTAACAAC-CT-TTATTTCAACATGGCGT-GTGAAAATATTTTTT
1 ATTTTTTTTTAACATGGCGTGTAACAACAATATTTTTTCAACATGGCGTAG-GAAAA-ATTCTTT
*
7745606 TCAAAATTACGTGTAGC-AA
64 TCAAAATGACGTGTAGCTAA
* * *
7745625 CA-TTTTTTTTATCATGGCGTGTAACAACAATATTTTTTCAACATGGCGTAGGACAACTTCTTTT
1 -ATTTTTTTTTAACATGGCGTGTAACAACAATATTTTTTCAACATGGCGTAGGAAAAATTCTTTT
** *
7745689 CACCATGAGGTGTAGCTAA
65 CAAAATGACGTGTAGCTAA
* *
7745708 ATTTTTTTTTAACATGGAGTGTAACAACAACATTTTT
1 ATTTTTTTTTAACATGGCGTGTAACAACAATATTTTT
7745745 CACCATGTGC
Statistics
Matches: 98, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
81 22 0.22
82 21 0.21
83 54 0.55
84 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (83 bp):
ATTTTTTTTTAACATGGCGTGTAACAACAATATTTTTTCAACATGGCGTAGGAAAAATTCTTTTC
AAAATGACGTGTAGCTAA
Found at i:7749038 original size:7 final size:7
Alignment explanation
Indices: 7749028--7749069 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
7749018 ATTTATCACC
7749028 TAAACCA
1 TAAACCA
7749035 TAAACCA
1 TAAACCA
*
7749042 TAAACCT
1 TAAACCA
7749049 TAAACGC-
1 TAAAC-CA
7749056 TAAACCA
1 TAAACCA
7749063 TAAACCA
1 TAAACCA
7749070 GTGCAATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 1 0.03
7 30 0.94
8 1 0.03
ACGTcount: A:0.52, C:0.29, G:0.02, T:0.17
Consensus pattern (7 bp):
TAAACCA
Found at i:7749640 original size:28 final size:29
Alignment explanation
Indices: 7749603--7749679 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
7749593 TCTTAATTGC
* *
7749603 TACACACCATGC-ATAATGACTAAGTTGT
1 TACACGCCATGCTAAAATGACTAAGTTGT
** *
7749631 TACACGCCATGCTTAAAATTCCTACGTTGT
1 TACACGCCATGC-TAAAATGACTAAGTTGT
7749661 TACACGCCATGTCTAAAAT
1 TACACGCCATG-CTAAAAT
7749680 TCATAAGATG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 11 0.27
30 29 0.71
31 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (29 bp):
TACACGCCATGCTAAAATGACTAAGTTGT
Found at i:7753343 original size:39 final size:40
Alignment explanation
Indices: 7753300--7753379 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
7753290 TTGTGAAAAC
* * *
7753300 ACCAATCGTGACGAGTTTA-AAAACT-TCACTAATGTAAAT
1 ACCAATCGTGACAAGATTAGAAAACTCT-ACTAAGGTAAAT
* *
7753339 ACCAATTGTGGCAAGATTAGAAAACTCTACTAAGGTAAAT
1 ACCAATCGTGACAAGATTAGAAAACTCTACTAAGGTAAAT
7753379 A
1 A
7753380 ATGGTCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 15 0.44
40 18 0.53
41 1 0.03
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (40 bp):
ACCAATCGTGACAAGATTAGAAAACTCTACTAAGGTAAAT
Found at i:7755642 original size:56 final size:56
Alignment explanation
Indices: 7755552--7755668 Score: 180
Period size: 56 Copynumber: 2.1 Consensus size: 56
7755542 CATCAAAAAA
* *
7755552 TGATTCTTGATGGAAAGGATTGGTATTATTCTCTTCATTGCTAAAGCTACTATTGT
1 TGATTCTTGATGGAAAGGATTGGTATTATCCTCTTCATCGCTAAAGCTACTATTGT
* * * *
7755608 TGATTCTTGATGGAAAGGATTGGTATTATCCTCTTCATCGTTGAAGTTCCTATTGT
1 TGATTCTTGATGGAAAGGATTGGTATTATCCTCTTCATCGCTAAAGCTACTATTGT
7755664 TGATT
1 TGATT
7755669 TGAGTAGTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (56 bp):
TGATTCTTGATGGAAAGGATTGGTATTATCCTCTTCATCGCTAAAGCTACTATTGT
Found at i:7763098 original size:16 final size:17
Alignment explanation
Indices: 7763077--7763115 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
7763067 TTACATAATG
7763077 ATTAAAT-ATATAAACA
1 ATTAAATAATATAAACA
* *
7763093 ATTAAATAATATTAATA
1 ATTAAATAATATAAACA
7763110 ATTAAA
1 ATTAAA
7763116 ACAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTAAATAATATAAACA
Found at i:7763112 original size:17 final size:16
Alignment explanation
Indices: 7763072--7763115 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
7763062 AGATTTTACA
*
7763072 TAATGATTAAATATAT
1 TAATAATTAAATATAT
* *
7763088 AAACAATTAAATAATAT
1 TAATAATTAAAT-ATAT
7763105 TAATAATTAAA
1 TAATAATTAAA
7763116 ACAAAGAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (16 bp):
TAATAATTAAATATAT
Found at i:7765860 original size:10 final size:10
Alignment explanation
Indices: 7765845--7765900 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
7765835 TCTGATACTT
7765845 TATAATGTAA
1 TATAATGTAA
7765855 TATAAT-TACA
1 TATAATGTA-A
7765865 TATAATGTAA
1 TATAATGTAA
*
7765875 TATGAT-TACA
1 TATAATGTA-A
*
7765885 AATAATGTAA
1 TATAATGTAA
7765895 TTATAA
1 -TATAA
7765901 ATAATGTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
9 4 0.11
10 25 0.68
11 8 0.22
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (10 bp):
TATAATGTAA
Found at i:7765870 original size:20 final size:20
Alignment explanation
Indices: 7765845--7765900 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
7765835 TCTGATACTT
7765845 TATAATGTAATATAATTACA
1 TATAATGTAATATAATTACA
*
7765865 TATAATGTAATATGATTACA
1 TATAATGTAATATAATTACA
*
7765885 AATAATGTAATTATAA
1 TATAATGTAA-TATAA
7765901 ATAATGTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (20 bp):
TATAATGTAATATAATTACA
Found at i:7765890 original size:15 final size:15
Alignment explanation
Indices: 7765872--7765945 Score: 87
Period size: 15 Copynumber: 4.9 Consensus size: 15
7765862 ACATATAATG
*
7765872 TAATATGATTACAAA
1 TAATATGATTATAAA
* *
7765887 TAATGTAATTATAAA
1 TAATATGATTATAAA
*
7765902 TAATGTGATTATAAA
1 TAATATGATTATAAA
7765917 TAATATGATTATAAA
1 TAATATGATTATAAA
*
7765932 AAATAAT-ATTATAA
1 TAAT-ATGATTATAA
7765946 TGTTTAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
15 50 0.96
16 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (15 bp):
TAATATGATTATAAA
Done.