Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009688.1 Kokia drynarioides strain JFW-HI SEQ_124406, 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: 112772
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:101 original size:2 final size:2
Alignment explanation
Indices: 59--89 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
49 TTGGTTGTAA
59 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90 TTTGATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:9170 original size:16 final size:16
Alignment explanation
Indices: 9138--9183 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
9128 GTTGAATCAA
*
9138 TAATTTATTTTATTTTT
1 TAATTT-TTTTAATTTT
9155 TAATTTTTTTAATTTT
1 TAATTTTTTTAATTTT
*
9171 TAATATTTTTAAT
1 TAATTTTTTTAAT
9184 CAAATTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TAATTTTTTTAATTTT
Found at i:12093 original size:24 final size:24
Alignment explanation
Indices: 12040--12113 Score: 59
Period size: 23 Copynumber: 3.2 Consensus size: 24
12030 AGCTTAATAT
*
12040 TATTATATTAATAATAAA-ATT-TAA
1 TATTA-ATTTATAA-AAATATTATAA
*
12064 TTTTAATTTATAAAAATATTATAA
1 TATTAATTTATAAAAATATTATAA
* *
12088 TATTAA-ATAT-TAAATATTA-AA
1 TATTAATTTATAAAAATATTATAA
12109 TATTA
1 TATTA
12114 TTAAACATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
21 7 0.16
22 11 0.26
23 13 0.30
24 12 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTAATTTATAAAAATATTATAA
Found at i:12098 original size:7 final size:7
Alignment explanation
Indices: 12077--12113 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
12067 TAATTTATAA
12077 AAATATT
1 AAATATT
12084 ATAATATT
1 A-AATATT
12092 AAATATT
1 AAATATT
12099 AAATATT
1 AAATATT
12106 AAATATT
1 AAATATT
12113 A
1 A
12114 TTAAACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAATATT
Found at i:12498 original size:23 final size:22
Alignment explanation
Indices: 12448--12507 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
12438 AATTTTAAAG
* *
12448 AATAATATTAATA-TATTATTT
1 AATAATATTTATATTAATATTT
*
12469 AAGAATATTTATATTAATATTTT
1 AATAATATTTATATTAATA-TTT
**
12492 AATAATAAATATATTA
1 AATAATATTTATATTA
12508 TAATTTACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 11 0.35
22 4 0.13
23 16 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
AATAATATTTATATTAATATTT
Found at i:12845 original size:20 final size:19
Alignment explanation
Indices: 12822--12861 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
12812 AAATATTACC
12822 TTTTTCAGAAAATCAATTTA
1 TTTTTCAG-AAATCAATTTA
*
12842 TTTTTCAGAAATCATTTTA
1 TTTTTCAGAAATCAATTTA
12861 T
1 T
12862 AGAAGTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTTTCAGAAATCAATTTA
Found at i:16246 original size:22 final size:21
Alignment explanation
Indices: 16218--16258 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
16208 TTACTTGTTG
*
16218 AAATTAGAGATGAATCATGATA
1 AAATTAGAGATAAAT-ATGATA
16240 AAATTAGAGATAAATATGA
1 AAATTAGAGATAAATATGA
16259 ATTAGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (21 bp):
AAATTAGAGATAAATATGATA
Found at i:17706 original size:22 final size:22
Alignment explanation
Indices: 17674--17719 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
17664 AAGCTTTGAT
*
17674 ATCATGTTGAAATTAGAGATGA
1 ATCATGATGAAATTAGAGATGA
17696 ATCATGATGAAATTAGAGATGA
1 ATCATGATGAAATTAGAGATGA
17718 AT
1 AT
17720 ACTGTAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.30
Consensus pattern (22 bp):
ATCATGATGAAATTAGAGATGA
Found at i:29653 original size:134 final size:137
Alignment explanation
Indices: 29409--29659 Score: 350
Period size: 136 Copynumber: 1.8 Consensus size: 137
29399 CTTTATTTAT
* * * *
29409 TACCAATCAAATAAGCAATTAGTAGAAGTTTTCATCAACATTATTGAACTTTATATTGAGATGGA
1 TACCAATCAAATAAGCAATTAGTAGAAGTGTTCATCAAAATTATCGAAATTTATATTGAGATGGA
*
29474 GGGGCATTGAAAATGGCCTATGTCTTAATGGAATATCACATCAGTTAGTAACCTATAATTCACCA
66 AGGGCATTGAAAATGGCC-ATGTCTTAATGGAATATCACATCAGTTAGTAACCTATAATTCACCA
29539 TTTGTTGA
130 TTTGTTGA
* * *
29547 TACCAATTAAATAAGCAATTAGT-GGAG-GTTCATCAAAATTATCGAAAATTT-TTTTGAGATGG
1 TACCAATCAAATAAGCAATTAGTAGAAGTGTTCATCAAAATTATCG-AAATTTATATTGAGATGG
* *
29609 AAGGGTATTGGAAAATGG-C-TGTCTTAATGGAATATCACTTCAGTTAGTAAC
65 AAGGGCATT-GAAAATGGCCATGTCTTAATGGAATATCACATCAGTTAGTAAC
29660 TTTGCCACAG
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
134 31 0.31
136 32 0.32
137 16 0.16
138 22 0.22
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (137 bp):
TACCAATCAAATAAGCAATTAGTAGAAGTGTTCATCAAAATTATCGAAATTTATATTGAGATGGA
AGGGCATTGAAAATGGCCATGTCTTAATGGAATATCACATCAGTTAGTAACCTATAATTCACCAT
TTGTTGA
Found at i:29959 original size:17 final size:18
Alignment explanation
Indices: 29925--29963 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
29915 AAAAGAAGAG
*
29925 AGAA-GAAAGACGATGGA
1 AGAAGGAAAGACGAGGGA
29942 AGAAGGAAAGAC-AGGGA
1 AGAAGGAAAGACGAGGGA
29959 AGAAG
1 AGAAG
29964 AAAAACCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.54, C:0.05, G:0.38, T:0.03
Consensus pattern (18 bp):
AGAAGGAAAGACGAGGGA
Found at i:33352 original size:13 final size:13
Alignment explanation
Indices: 33328--33363 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
33318 ATATATTTGT
33328 AGTATGTTTAGTTA
1 AGTAT-TTTAGTTA
33342 AGTATTTTAGTTA
1 AGTATTTTAGTTA
33355 AGTATTTTA
1 AGTATTTTA
33364 ATTAGTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.53
Consensus pattern (13 bp):
AGTATTTTAGTTA
Found at i:34927 original size:29 final size:30
Alignment explanation
Indices: 34886--34942 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
34876 CGTATCAAAC
*
34886 TAGTCATTTTATTATTAAAAT-AATCAATT
1 TAGTCATTCTATTATTAAAATGAATCAATT
*
34915 TAGTCCTTCTATTATTAAAATGAATCAA
1 TAGTCATTCTATTATTAAAATGAATCAA
34943 ACAAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (30 bp):
TAGTCATTCTATTATTAAAATGAATCAATT
Found at i:40315 original size:440 final size:440
Alignment explanation
Indices: 39493--40812 Score: 1980
Period size: 440 Copynumber: 3.0 Consensus size: 440
39483 GCGCTAGTGG
* * * * *
39493 CACCACTGTCAAGGTACTATGCCTGATCCATCACTGTTCTTGGGGTAGCAAGCATAGCAGTAGGA
1 CACCACTGTCAGGGTACCATGCCTGATCCACCACTGTTCTTGGAGTAGCAAGCATGGCAGTAGGA
* * ** * * *
39558 CCATTGCATGATACAGGTGTGACTCCAGAATTGACAACTATTTGTGAAGCTTGAGAAAACTGTAC
66 CCATTGCATGATACAGGTGTGACTCAAGAATTGACAACTATTCGCAAAGCATGAGAAGACTGCAC
* * * * *
39623 AATTGAACCTGCATAGAGAGACTGCATAATCGGAGTTGCAGGTTTAACATAGTAATATTGAGCCA
131 AACTGAACCTGCATAGAGAGACTGCATAACCGGAGATGCAGGTTCAACACAGTAATATTGAGCCA
* * *
39688 TATGTCTCATAGGAGCTTGAAACTCACGTGAGGATGAAGGAGACTCAAACTCAGTGTCATCCTCA
196 TATGTCTCACAGAAGCTTGAAACCCACGTGAGGATGAAGGAGACTCAAACTCAGTGTCATCCTCA
*
39753 TAACTATAAAAGCATCGTCGAGCCACATGTCCCACGCGATCACAAATTGGACATTGTGGACGCGA
261 TAACTATAAAAGCATCGTCGAGCCACATGTCCCACGCGATCACAAATTTGACATTGTGGACGCGA
*
39818 ACCATGAACAAAATTACCACGAGCACGACCCCTACTGAAACCACCAGCTCATCCAATCCTAAATG
326 ACCACGAACAAAATTACCACGAGCACGACCCCTACTGAAACCACCAGCTCATCCAATCCTAAATG
39883 TTTGAGTCTCTGAATTATCAGTCTGAATCTGACCTGAAGGTGCAGCTGTC
391 TTTGAGTCTCTGAATTATCAGTCTGAATCTGACCTGAAGGTGCAGCTGTC
* *
39933 CACCACTATCAGGGTACCATGCCTGATCCACCACTGTTCTTGGAGAAGCAAGCATGGCAGTAGGA
1 CACCACTGTCAGGGTACCATGCCTGATCCACCACTGTTCTTGGAGTAGCAAGCATGGCAGTAGGA
* * * *
39998 TCATTGTATGATACAGGTGTGACTCTAGAATTGACAACTATTCGCAAAGCCTGAGAAGACTGCAC
66 CCATTGCATGATACAGGTGTGACTCAAGAATTGACAACTATTCGCAAAGCATGAGAAGACTGCAC
* * *
40063 AACTGAACCTGCATAGAAAGACTGCATAACCGGAGATACAGGTTCAACACAGTAATATTGGGCCA
131 AACTGAACCTGCATAGAGAGACTGCATAACCGGAGATGCAGGTTCAACACAGTAATATTGAGCCA
* * * *
40128 TATGTCTCACAGAATCTTGAAACCCGCATGAGGATGAAGGAGACTCAAACTCAGTGTCATCTTCA
196 TATGTCTCACAGAAGCTTGAAACCCACGTGAGGATGAAGGAGACTCAAACTCAGTGTCATCCTCA
* *
40193 TAACTATAAAAGTATCGTCGAGCCACATGTCCCACGCGATCACAAATTTGACATTGTGGATGCGA
261 TAACTATAAAAGCATCGTCGAGCCACATGTCCCACGCGATCACAAATTTGACATTGTGGACGCGA
* * *
40258 ACCACGAACAAAATGACCACAAGCACGACCCCTACTGAAACCACCAGCTCGTCCAATCCTAAATG
326 ACCACGAACAAAATTACCACGAGCACGACCCCTACTGAAACCACCAGCTCATCCAATCCTAAATG
* * *
40323 TTCGAGTCTCTGAATTATCAGACTGAATTTGACCT-AGAGGTGCAGCTGTC
391 TTTGAGTCTCTGAATTATCAGTCTGAATCTGACCTGA-AGGTGCAGCTGTC
* * *
40373 CACCACTGTCAGGGTACCATGCCTAATCCACCACTGTTCTT-GAGGTAGCAAGCATGGTAGTAAG
1 CACCACTGTCAGGGTACCATGCCTGATCCACCACTGTTCTTGGA-GTAGCAAGCATGGCAGTAGG
* * *
40437 ACCATTGCATGATACAGGTGTGACTCAAAAATTGACAACTAGTCGCAAAGCATGACAAGACTGCA
65 ACCATTGCATGATACAGGTGTGACTCAAGAATTGACAACTATTCGCAAAGCATGAGAAGACTGCA
* * * * *
40502 CATCTGAACTTGCATAGAGAGATTGCATAACCGGAGCTGCAGGTTCAACACAGCAATATTGAGCC
130 CAACTGAACCTGCATAGAGAGACTGCATAACCGGAGATGCAGGTTCAACACAGTAATATTGAGCC
40567 ATATGTCTCACA-AGAGCTTGAAACCCACGTGAGGATGAAGGAGACTCAAACTCAGTGTCATCCT
195 ATATGTCTCACAGA-AGCTTGAAACCCACGTGAGGATGAAGGAGACTCAAACTCAGTGTCATCCT
* * * * *
40631 CATAACTATAAAAGCATCGCCGAGCCACATGTCCTACGTGATCACAAATTTAACATTATGGACGC
259 CATAACTATAAAAGCATCGTCGAGCCACATGTCCCACGCGATCACAAATTTGACATTGTGGACGC
* * *
40696 AAACCACAAACAAAATTACCACGAGCGCGACCCCTACTGAAACCACCAGCTCATCCAATCCTAAA
324 GAACCACGAACAAAATTACCACGAGCACGACCCCTACTGAAACCACCAGCTCATCCAATCCTAAA
* * * * * *
40761 TGTTTTAGCCCCTGAATTATCAGTCTGAATCTGACCTGGAGGTACAACTGTC
389 TGTTTGAGTCTCTGAATTATCAGTCTGAATCTGACCTGAAGGTGCAGCTGTC
40813 TGTGAAACCA
Statistics
Matches: 789, Mismatches: 87, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
439 4 0.01
440 785 0.99
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (440 bp):
CACCACTGTCAGGGTACCATGCCTGATCCACCACTGTTCTTGGAGTAGCAAGCATGGCAGTAGGA
CCATTGCATGATACAGGTGTGACTCAAGAATTGACAACTATTCGCAAAGCATGAGAAGACTGCAC
AACTGAACCTGCATAGAGAGACTGCATAACCGGAGATGCAGGTTCAACACAGTAATATTGAGCCA
TATGTCTCACAGAAGCTTGAAACCCACGTGAGGATGAAGGAGACTCAAACTCAGTGTCATCCTCA
TAACTATAAAAGCATCGTCGAGCCACATGTCCCACGCGATCACAAATTTGACATTGTGGACGCGA
ACCACGAACAAAATTACCACGAGCACGACCCCTACTGAAACCACCAGCTCATCCAATCCTAAATG
TTTGAGTCTCTGAATTATCAGTCTGAATCTGACCTGAAGGTGCAGCTGTC
Found at i:42290 original size:42 final size:41
Alignment explanation
Indices: 42227--42310 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
42217 AACTTATTAA
*
42227 AAGTTGTTATTTTATTTATTTTATTTTGACTAAATTATATTT
1 AAGTTGTTATTTTATTAATTTTATTTTGACTAAATT-TATTT
* *
42269 AAGTTGTTATTTTCTTAATTTTATTTTTACTAAATTTATTT
1 AAGTTGTTATTTTATTAATTTTATTTTGACTAAATTTATTT
42310 A
1 A
42311 TTTTAGGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 6 0.15
42 33 0.85
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.62
Consensus pattern (41 bp):
AAGTTGTTATTTTATTAATTTTATTTTGACTAAATTTATTT
Found at i:49156 original size:66 final size:66
Alignment explanation
Indices: 49079--49203 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
49069 ATTTTTTTTT
49079 TATGAATATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTA-TTATTTATTTATTAT
1 TATGAATATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTATTTA-TTATTTATTAT
49143 TG
65 TG
49145 TATGAATATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTATTTATTATTT
1 TATGAATATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTATTTATTATTT
49204 TATGAATATA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
66 55 0.95
67 3 0.05
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (66 bp):
TATGAATATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTATTTATTATTTATTATT
G
Found at i:49195 original size:59 final size:61
Alignment explanation
Indices: 49079--49230 Score: 209
Period size: 59 Copynumber: 2.4 Consensus size: 61
49069 ATTTTTTTTT
49079 TATGAATATAAATAAATATAAAATAATATTAATTTTGTTTTATTATTTATTATTTATTTATTATT
1 TATGAATATAAATAAATATAAAATAATATTAATTTTG-----TTATTTATTATTTATTTATTATT
49144 G
61 G
*
49145 TATGAATATAAATAAATATAAAATAATATTAATTTTG-T-TTTATTATTTATTTATTATTT
1 TATGAATATAAATAAATATAAAATAATATTAATTTTGTTATTTATTATTTATTTATTATTG
* *
49204 TATGAATATAGATAAATAAATAAATAA
1 TATGAATATAAATAAATATA-AAATAA
49231 ATAACAAAAT
Statistics
Matches: 82, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
59 38 0.46
60 7 0.09
66 37 0.45
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (61 bp):
TATGAATATAAATAAATATAAAATAATATTAATTTTGTTATTTATTATTTATTTATTATTG
Found at i:55654 original size:40 final size:40
Alignment explanation
Indices: 55568--55656 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
55558 TACAATCATC
* *
55568 CAATCTTTTACCCTAATCAAAAGGTAGATTGAAGACCATT
1 CAATCTTTTACCCTAATCAAAAGGCAGATTGAAGAACATT
* * *
55608 CAATCTTTTACCTTAATCAGATGGCAGATTGAA-AAC-TGT
1 CAATCTTTTACCCTAATCAAAAGGCAGATTGAAGAACAT-T
55647 CAGATCTTTT
1 CA-ATCTTTT
55657 TAAAGACCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.02
39 5 0.12
40 36 0.86
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (40 bp):
CAATCTTTTACCCTAATCAAAAGGCAGATTGAAGAACATT
Found at i:55721 original size:20 final size:20
Alignment explanation
Indices: 55696--55736 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
55686 AGAGGGCAGA
55696 TTGAAGACCATC-AGATCTTT
1 TTGAAGACCATCTA-ATCTTT
55716 TTGAAGACCATCTAATCTTT
1 TTGAAGACCATCTAATCTTT
55736 T
1 T
55737 ACCCTAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (20 bp):
TTGAAGACCATCTAATCTTT
Found at i:55761 original size:60 final size:60
Alignment explanation
Indices: 55596--55761 Score: 226
Period size: 60 Copynumber: 2.8 Consensus size: 60
55586 AAAAGGTAGA
* * * * **
55596 TTGAAGACCAT-TCAATCTTTTACCTTAATCAGATGGCAGATTGAAAACTGTCAGATCTTT
1 TTGAAGACCATCT-AATCTTTTACCCTAACCAGAAGGCAGATTGAAGACCATCAGATCTTT
* * *
55656 TTAAAGACCATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCAGATCTTT
1 TTGAAGACCATCTAATCTTTTACCCTAACCAGAAGGCAGATTGAAGACCATCAGATCTTT
*
55716 TTGAAGACCATCTAATCTTTTACCCTAACCAGAAGGCAAATTGAAG
1 TTGAAGACCATCTAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
55762 CAGTCCAATC
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (60 bp):
TTGAAGACCATCTAATCTTTTACCCTAACCAGAAGGCAGATTGAAGACCATCAGATCTTT
Found at i:55773 original size:39 final size:38
Alignment explanation
Indices: 55724--56962 Score: 545
Period size: 39 Copynumber: 31.4 Consensus size: 38
55714 TTTTGAAGAC
* *
55724 CATCTAATCTTTTACCCTAACCAGAAGGCAAATTGAAG
1 CATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
55762 CAGTCCAATCTTTTACCCTAA-CAGAAGGCAGATTGAAG
1 CA-TCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
* * * *
55800 CCATCCAATCTCTTACCCTGACCATG-AGGCAAATTCAAG
1 -CATCCAATCTTTTACCCTAACCA-GAAGGCAGATTGAAG
* * *
55839 CAATCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAAAC
1 C-ATCCAATCTTTTACCCTAACCAGAAGGCAGATTG--AAG
* * ** * * *
55880 CATCCGATCTCTTACCCCGATCA-AAGGGCAGATTAAAAAC
1 CATCCAATCTTTTACCCTAACCAGAA-GGCAGATT--GAAG
*
55920 CATCAAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
1 CATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
* * * *
55958 CCATCCAATCTCTTACTCC-GACCATG-GGGCAAATTGAAG
1 -CATCCAATCTTTTAC-CCTAACCA-GAAGGCAGATTGAAG
* * * *
55997 CAATCTAATATTTTACCCTAACCAGAGGGTAGATTGAAG
1 C-ATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
* * * *
56036 ACATCCTACCTTTTACTCC-GACCA-AAGGGCAAATTGAAG
1 -CATCCAATCTTTTAC-CCTAACCAGAA-GGCAGATTGAAG
* * * *
56075 ACCATCCGATCTCTTACCCCAACCATG-GGGCAGATTGAAG
1 --CATCCAATCTTTTACCCTAACCA-GAAGGCAGATTGAAG
* * *
56115 TAATTCAGATCTTTTACCC-AAACAG-AGAGCAGATTGAAG
1 -CATCCA-ATCTTTTACCCTAACCAGAAG-GCAGATTGAAG
* * * * *
56154 TAATCTAGACCTTTTACCCTAACTAGAAGGAAGATTGAATAG
1 -CATCCA-ATCTTTTACCCTAACCAGAAGGCAGATTG-A-AG
* * * *
56196 CATTCAATCTCTTACCCCAACCATG-GGGACA-ATTGAAG
1 CATCCAATCTTTTACCCTAACCA-GAAGG-CAGATTGAAG
* *
56234 CAGTCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
1 CA-TCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
* * * *
56273 TCATCTAATCTCTTACCCTGATCATG-AGGCAGATTGAAG
1 -CATCCAATCTTTTACCCTAACCA-GAAGGCAGATTGAAG
* *
56312 CAATCCAATCTTTTACCCTAACCAGAGGGCAGATTAAAG
1 C-ATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
* * ** *
56351 ACCATCTAATCTCTTACCTCGGA-CAG-AGGAAAGATTGAAGG
1 --CATCCAATCTTTTACC-CTAACCAGAAGG-CAGATTGAA-G
* * * *
56392 CTATCCGATCTCTTACCCTGACCATG-GGGCAGATTGAAG
1 C-ATCCAATCTTTTACCCTAACCA-GAAGGCAGATTGAAG
* * *
56431 ACCATCCGATCTTTTACCCTAATCAGAGGGCAGATTGAAG
1 --CATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
* * * * *
56471 CCATCCAATCTCTTACCTTGACCATG-GGGTAGATTGAAG
1 -CATCCAATCTTTTACCCTAACCA-GAAGGCAGATTGAAG
* * * *
56510 CAATCCAATCTTTTAACCTAATCAGAGGGTAGATTGAAG
1 C-ATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
* * * **
56549 ATCACCCGATCTCTTACCCCGACCAG-AGAGCAGATTGAAG
1 --CATCCAATCTTTTACCCTAACCAGAAG-GCAGATTGAAG
* * * *
56589 ACCATCCGATCTTTTACCTTGAA-CATG-GGGCAGATTAAAG
1 --CATCCAATCTTTTACCCT-AACCA-GAAGGCAGATTGAAG
** *
56629 ACCATCCAATCTTTTACCCCGACCAGACGGCAGATTGAAG
1 --CATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
* * * *
56669 ACCATCCGATCTCTTACCCCAACC-GTGAGGCAGATTGAAG
1 --CATCCAATCTTTTACCCTAACCAG-AAGGCAGATTGAAG
* ** * * * *
56709 TAATTTAGATCTTTTACCCTAATCA-AAGGGTATATTAAAG
1 -CATCCA-ATCTTTTACCCTAACCAGAA-GGCAGATTGAAG
* * ** *
56749 TAATCCAGATCTGTTACCCCGATCATG-AGGCAGATTGAAG
1 -CATCCA-ATCTTTTACCCTAACCA-GAAGGCAGATTGAAG
** * *
56789 CCAT-CAGATCTTTTACCCCGATCATG-AGGTAGATTGAAG
1 -CATCCA-ATCTTTTACCCTAACCA-GAAGGCAGATTGAAG
* * *
56828 CAATCCAATCTTTTATCCTAACAAGAGGGCAGATTGAAG
1 C-ATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
* ** * * * *
56867 ACCATCCAATTCTGTTACCCCGA-TATG-GGGCAAATTGTAG
1 --CATCCAA-TCTTTTACCCTAACCA-GAAGGCAGATTGAAG
* *
56907 CAATCCAATCTTTTACCCTAACTAG-AGGCAAATTGAAG
1 C-ATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
**
56945 ACCATCTGATCTTTTACC
1 --CATCCAATCTTTTACC
56963 TCGACTGTGG
Statistics
Matches: 933, Mismatches: 190, Indels: 155
0.73 0.15 0.12
Matches are distributed among these distances:
38 81 0.09
39 415 0.44
40 398 0.43
41 37 0.04
42 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (38 bp):
CATCCAATCTTTTACCCTAACCAGAAGGCAGATTGAAG
Found at i:55969 original size:158 final size:157
Alignment explanation
Indices: 55716--56886 Score: 779
Period size: 158 Copynumber: 7.4 Consensus size: 157
55706 TCAGATCTTT
* * * ** * *
55716 TTGAAGACCATCTAATCTTTTACCCTAACCAGAA-GGCAAATTGAAG--CAGTCCAATCTTTTAC
1 TTGAAAACCATCCAATCTCTTACCCCGACCA-AAGGGCAGATTGAAGACCA-TCCAATCTCTTAC
* * *
55778 CCTAA-CAGAAGGCAGATTGAAGCCATCCAATCTCTTACCCTGACCATGAGGCAAATTCAAGCAA
64 CCTAACCAG-AGGCAGATTGAAGCCATCCAATCTCTTACCCTGAACATGAGGCAGATTGAAGCAA
*
55842 TCTAATCTTTTACCCTAACCAGAGGGCAGA
128 TCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * * * *
55872 TTGAAAACCATCCGATCTCTTACCCCGATCAAAGGGCAGATTAAAAACCATCAAATCTTTTACCC
1 TTGAAAACCATCCAATCTCTTACCCCGACCAAAGGGCAGATTGAAGACCATCCAATCTCTTACCC
* * *
55937 TAACCAGAAGGCAGATTGAAGCCATCCAATCTCTTACTCC-GACCATGGGGCAAATTGAAGCAAT
66 TAACCAG-AGGCAGATTGAAGCCATCCAATCTCTTAC-CCTGAACATGAGGCAGATTGAAGCAAT
* * *
56001 CTAATATTTTACCCTAACCAGAGGGTAGA
129 CCAATCTTTTACCCTAACCAGAGGGCAGA
* * * * * * *
56030 TTGAAGA-CATCCTACCTTTTACTCCGACCAAAGGGCAAATTGAAGACCATCCGATCTCTTACCC
1 TTGAAAACCATCCAATCTCTTACCCCGACCAAAGGGCAGATTGAAGACCATCCAATCTCTTACCC
* * ** * * * *
56094 CAACCATGGGGCAGATTGAAGTAATTCAGATCTTTTACCC-AAACA-GAGAGCAGATTGAAGTAA
66 TAACCA-GAGGCAGATTGAAGCCATCCA-ATCTCTTACCCTGAACATGAG-GCAGATTGAAGCAA
* * * * *
56157 TCTAGACCTTTTACCCTAACTAGAAGGAAGA
128 TCCA-ATCTTTTACCCTAACCAGAGGGCAGA
* * * * ** * *
56188 TTGAATAGCATTCAATCTCTTACCCCAACCATGGGGACA-ATTGAAG--CAGTCTAATCTTTTAC
1 TTGAAAACCATCCAATCTCTTACCCCGACCAAAGGG-CAGATTGAAGACCA-TCCAATCTCTTAC
* * *
56250 CCTAACCAGAGGGCAGATTGAAGTCATCTAATCTCTTACCCTGATCATGAGGCAGATTGAAGCAA
64 CCTAACCAGA-GGCAGATTGAAGCCATCCAATCTCTTACCCTGAACATGAGGCAGATTGAAGCAA
56315 TCCAATCTTTTACCCTAACCAGAGGGCAGA
128 TCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * ** * * *
56345 TT-AAAGACCATCTAATCTCTTACCTCGGA-CAGAGGAAAGATTGAAGGCTATCCGATCTCTTAC
1 TTGAAA-ACCATCCAATCTCTTACC-CCGACCAAAGGGCAGATTGAAGACCATCCAATCTCTTAC
* * * *
56408 CCTGACCATGGGGCAGATTGAAGACCATCCGATCTTTTACCCT-AATCA-GAGGGCAGATTGAAG
64 CCTAACCA-GAGGCAGATTGAAG-CCATCCAATCTCTTACCCTGAA-CATGA-GGCAGATTGAAG
* * * * *
56471 CCATCCAATCTCTTACCTTGACCATG-GGGTAGA
125 CAATCCAATCTTTTACCCTAACCA-GAGGGCAGA
* * * * ** * * * * * *
56504 TTG-AAGCAATCCAATCTTTTAACCTAATCAGAGGGTAGATTGAAGATCACCCGATCTCTTACCC
1 TTGAAAACCATCCAATCTCTTACCCCGACCAAAGGGCAGATTGAAGACCATCCAATCTCTTACCC
** * * * * * *
56568 CGACCAGAGAGCAGATTGAAGACCATCCGATCTTTTACCTTGAACATGGGGCAGATTAAAGACCA
66 TAACCAGAG-GCAGATTGAAG-CCATCCAATCTCTTACCCTGAACATGAGGCAGATTGAAG-CAA
** *
56633 TCCAATCTTTTACCCCGACCAGACGGCAGA
128 TCCAATCTTTTACCCTAACCAGAGGGCAGA
* * * ** ** *
56663 TTGAAGACCATCCGATCTCTTACCCCAACC-GTGAGGCAGATTGAAGTA--ATTTAGATCTTTTA
1 TTGAAAACCATCCAATCTCTTACCCCGACCAAAG-GGCAGATTGAAG-ACCATCCA-ATCTCTTA
* * * * * ** * * *
56725 CCCTAATCAAAGGGTATATTAAAGTAATCCAGATCTGTTACCCCGATCATGAGGCAGATTGAAGC
63 CCCTAACCAGA-GGCAGATTGAAGCCATCCA-ATCTCTTACCCTGAACATGAGGCAGATTGAAGC
* ** * *
56790 CAT-CAGATCTTTTACCCCGATCATGA-GGTAGA
126 AATCCA-ATCTTTTACCCTAACCA-GAGGGCAGA
* * * * * * *
56822 TTG-AAGCAATCCAATCTTTTA-TCCTAACAAGAGGGCAGATTGAAGACCATCCAATTCTGTTAC
1 TTGAAAACCATCCAATCTCTTACCCCGACCAA-AGGGCAGATTGAAGACCATCCAA-TCTCTTAC
56885 CC
64 CC
56887 CGATATGGGG
Statistics
Matches: 806, Mismatches: 164, Indels: 87
0.76 0.16 0.08
Matches are distributed among these distances:
155 2 0.00
156 38 0.05
157 177 0.22
158 332 0.41
159 173 0.21
160 82 0.10
161 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (157 bp):
TTGAAAACCATCCAATCTCTTACCCCGACCAAAGGGCAGATTGAAGACCATCCAATCTCTTACCC
TAACCAGAGGCAGATTGAAGCCATCCAATCTCTTACCCTGAACATGAGGCAGATTGAAGCAATCC
AATCTTTTACCCTAACCAGAGGGCAGA
Found at i:56210 original size:119 final size:115
Alignment explanation
Indices: 55928--56866 Score: 430
Period size: 119 Copynumber: 7.9 Consensus size: 115
55918 ACCATCAAAT
* * *
55928 CTTTTACCCTAACCAGAAGGCAGATTG-AAGCCATCCAATCTCTTACTCCGACCATGGGGCAAAT
1 CTTTTACCCTAACCAGAAGGAAGATTGAAAG-CATCCAATCTCTTACCCCAACCATGGGGC-AAT
* *
55992 TGAAGCAATCTAATATTTTACCCTAACCAGAGGGTAGATTGAAG-ACATCCT-AC
64 TGAAG-AATCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAGTA-AT-CTAAC
* * *
56045 CTTTTACTCC-GACCA-AAGGGCAA-ATTGAAGACCATCCGATCTCTTACCCCAACCATGGGGCA
1 CTTTTAC-CCTAACCAGAA-GG-AAGATTGAA-AGCATCCAATCTCTTACCCCAACCATGGGGCA
* *
56107 GATTGAAGTAAT-TCAGATCTTTTACCC-AAACAGAGAGCAGATTGAAGTAATCTAGAC
62 -ATTGAAG-AATCT-A-ATCTTTTACCCTAACCAGAGGGCAGATTGAAGTAATCTA-AC
* *
56164 CTTTTACCCTAACTAGAAGGAAGATTGAATAGCATTCAATCTCTTACCCCAACCATGGGGACAAT
1 CTTTTACCCTAACCAGAAGGAAGATTGAA-AGCATCCAATCTCTTACCCCAACCATGGGG-CAAT
* * *
56229 TGAAGCAGTCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAGTCATCTAAT
64 TGAAG-AATCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAGTAATCTAAC
* * * * * *
56282 CTCTTACCCTGATCATG-AGGCAGATTG-AAGCAATCCAATCTTTTACCCTAACCA-GAGGGCAG
1 CTTTTACCCTAACCA-GAAGGAAGATTGAAAGC-ATCCAATCTCTTACCCCAACCATG-GGGCA-
* * ** ** ** *
56344 ATTAAAGACCATCTAATCTCTTACCTCGGA-CAGAGGAAAGATTGAAGGCT-ATCCGAT
62 ATTGAAGA--ATCTAATCTTTTACC-CTAACCAGAGGGCAGATTGAA-G-TAATCTAAC
* * * * * * * * *
56401 CTCTTACCCTGACCATG-GGGCAGATTGAAGACCATCCGATCTTTTACCCTAATCA-GAGGGCAG
1 CTTTTACCCTAACCA-GAAGGAAGATTGAA-AGCATCCAATCTCTTACCCCAACCATG-GGGCA-
* * * * * * * * *
56464 ATTGAAGCCATCCAATCTCTTACCTTGACCATG-GGGTAGATTGAAGCAATCCAAT
62 ATTGAAG-AATCTAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGTAATCTAAC
* * * * * * * * *
56519 CTTTTAACCTAATCAGAGGGTAGATTGAAGATCACCCGATCTCTTACCCCGACCA-GAGAGCAGA
1 CTTTTACCCTAACCAGAAGGAAGATTGAA-AGCATCCAATCTCTTACCCCAACCATG-GGGCA-A
** * * * *
56583 TTGAAGACCATCCGATCTTTTACCTTGAA-CATG-GGGCAGATTAAAG-ACCATCCAAT
63 TTGAAGA--ATCTAATCTTTTACCCT-AACCA-GAGGGCAGATTGAAGTA--ATCTAAC
** * * * * * *
56639 CTTTTACCCCGACCAGACGGCAGATTGAAGACCATCCGATCTCTTACCCCAACCGTGAGGCAGAT
1 CTTTTACCCTAACCAGAAGGAAGATTGAA-AGCATCCAATCTCTTACCCCAACCATGGGGCA-AT
* * * * * * * *
56704 TGAAGTAATTTAGATCTTTTACCCTAATCAAAGGGTATATTAAAGTAATCCAGAT
64 TGAAG-AATCTA-ATCTTTTACCCTAACCAGAGGGCAGATTGAAGTAATCTA-AC
* ** * * * * * * *
56759 CTGTTACCCCGATCATG-AGGCAGATTG-AAGCCAT-CAGATCTTTTACCCCGATCATGAGGTAG
1 CTTTTACCCTAACCA-GAAGGAAGATTGAAAG-CATCCA-ATCTCTTACCCCAACCATGGGGCA-
* * *
56821 ATTGAAGCAATCCAATCTTTTATCCTAACAAGAGGGCAGATTGAAG
62 ATTGAAG-AATCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAG
56867 ACCATCCAAT
Statistics
Matches: 663, Mismatches: 111, Indels: 95
0.76 0.13 0.11
Matches are distributed among these distances:
116 9 0.01
117 51 0.08
118 216 0.33
119 227 0.34
120 154 0.23
121 6 0.01
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (115 bp):
CTTTTACCCTAACCAGAAGGAAGATTGAAAGCATCCAATCTCTTACCCCAACCATGGGGCAATTG
AAGAATCTAATCTTTTACCCTAACCAGAGGGCAGATTGAAGTAATCTAAC
Found at i:57000 original size:78 final size:77
Alignment explanation
Indices: 56382--57002 Score: 355
Period size: 80 Copynumber: 7.9 Consensus size: 77
56372 GACAGAGGAA
* * * * * * * * *
56382 AGATTGAAGGCTATCCGATCTCTTACCCTGACCATGGGGCAGATTGAAGACCATCCGATCTTTTA
1 AGATTGAAGACCATCAGATCTTTTACCCCGA-TATGGGGTAGATTGAAG-CAATCCAATCTTTTA
56447 CCCTAATC-AGAGGGC
64 CCCTAA-CAAGA-GGC
* ** *
56462 AGATTGAAG-CCATCCA-ATCTCTTACCTTGACCATGGGGTAGATTGAAGCAATCCAATCTTTTA
1 AGATTGAAGACCAT-CAGATCTTTTACCCCGA-TATGGGGTAGATTGAAGCAATCCAATCTTTTA
* *
56525 ACCTAATC-AGAGGGT
64 CCCTAA-CAAGA-GGC
* * * * * * * * *
56540 AGATTGAAGATCACCCGATCTCTTACCCCGACCA-GAGAGCAGATTGAAGACCATCCGATCTTTT
1 AGATTGAAGACCATCAGATCTTTTACCCCGA-TATG-GGGTAGATTGAAG-CAATCCAATCTTTT
* * *
56604 ACCTTGAACATGGGGC
63 ACCCT-AACAAGAGGC
* * * * * * *
56620 AGATTAAAGACCATCCA-ATCTTTTACCCCGACCA-GACGGCAGATTGAAGACCATCCGATCTCT
1 AGATTGAAGACCAT-CAGATCTTTTACCCCGA-TATG-GGGTAGATTGAAG-CAATCCAATCTTT
* **
56683 TACCCCAACCGTGAGGC
62 TACCCTAA-CAAGAGGC
* ** ** * * * *
56700 AGATTGAAGTA--ATTTAGATCTTTTACCCTAATCAAAGGGTATATTAAAGTAATCCAGATCTGT
1 AGATTGAAG-ACCA-TCAGATCTTTTACCCCGAT-ATGGGGTAGATTGAAGCAATCCA-ATCTTT
* * *
56763 TACCCCGATCATGAGGC
62 TA-CCCTAACAAGAGGC
* *
56780 AGATTGAAG-CCATCAGATCTTTTACCCCGATCATGAGGTAGATTGAAGCAATCCAATCTTTTAT
1 AGATTGAAGACCATCAGATCTTTTACCCCGAT-ATGGGGTAGATTGAAGCAATCCAATCTTTTAC
56844 CCTAACAAGAGGGC
65 CCTAACAAGA-GGC
* * * *
56858 AGATTGAAGACCATCCA-ATTCTGTTACCCCGATATGGGGCAAATTGTAGCAATCCAATCTTTTA
1 AGATTGAAGACCAT-CAGA-TCTTTTACCCCGATATGGGGTAGATTGAAGCAATCCAATCTTTTA
*
56922 CCCTAACTAGAGGC
64 CCCTAACAAGAGGC
* * * * * * *
56936 AAATTGAAGACCATCTGATCTTTTACCTCGACTGTGGGGTAGATTAAAGTAATCTAATCTTTTAC
1 AGATTGAAGACCATCAGATCTTTTACCCCGA-TATGGGGTAGATTGAAGCAATCCAATCTTTTAC
57001 CC
65 CC
57003 CTAAAGCTAT
Statistics
Matches: 434, Mismatches: 83, Indels: 50
0.77 0.15 0.09
Matches are distributed among these distances:
77 19 0.04
78 101 0.23
79 144 0.33
80 161 0.37
81 9 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (77 bp):
AGATTGAAGACCATCAGATCTTTTACCCCGATATGGGGTAGATTGAAGCAATCCAATCTTTTACC
CTAACAAGAGGC
Found at i:58244 original size:12 final size:12
Alignment explanation
Indices: 58227--58253 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58217 TAATAGTAAT
58227 TTTGTTTTATTA
1 TTTGTTTTATTA
58239 TTTGTTTTATTA
1 TTTGTTTTATTA
58251 TTT
1 TTT
58254 TATGAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (12 bp):
TTTGTTTTATTA
Found at i:63151 original size:29 final size:29
Alignment explanation
Indices: 63103--63158 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
63093 TTAGTAGTTT
63103 AGCTCATCAAAGGGAAACTGAAACCTTTC
1 AGCTCATCAAAGGGAAACTGAAACCTTTC
*
63132 AGCTCATCGAAA-GGAGACTGAAACCTT
1 AGCTCATC-AAAGGGAAACTGAAACCTT
63159 GGGACTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (29 bp):
AGCTCATCAAAGGGAAACTGAAACCTTTC
Found at i:67289 original size:36 final size:38
Alignment explanation
Indices: 67233--67304 Score: 130
Period size: 36 Copynumber: 1.9 Consensus size: 38
67223 AAAAAAATAA
67233 ATATTTTAAAAAAAGAGAGGTCAATTTTTTAAAGCTAG
1 ATATTTTAAAAAAAGAGAGGTCAATTTTTTAAAGCTAG
67271 ATATTTT-AAAAAA-AGAGGTCAATTTTTTAAAGCT
1 ATATTTTAAAAAAAGAGAGGTCAATTTTTTAAAGCT
67305 GCTTGTGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 21 0.62
37 6 0.18
38 7 0.21
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (38 bp):
ATATTTTAAAAAAAGAGAGGTCAATTTTTTAAAGCTAG
Found at i:72970 original size:50 final size:50
Alignment explanation
Indices: 72895--72989 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
72885 AAAGTGATTG
*
72895 AAAATGAAAGCATTGTGTTAATGGATCAGAACCCTTAGTTTCATCACTTT
1 AAAATAAAAGCATTGTGTTAATGGATCAGAACCCTTAGTTTCATCACTTT
*
72945 AAAATAAAAGCATTGTGTCT-ATGGATGAGAACCCTTAGTTTCATC
1 AAAATAAAAGCATTGTGT-TAATGGATCAGAACCCTTAGTTTCATC
72990 TGCATGGGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 41 0.98
51 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (50 bp):
AAAATAAAAGCATTGTGTTAATGGATCAGAACCCTTAGTTTCATCACTTT
Found at i:79661 original size:17 final size:18
Alignment explanation
Indices: 79626--79664 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
79616 AATATTACAG
*
79626 AAAATAGTTCTGAAGATA
1 AAAATAATTCTGAAGATA
*
79644 AAAATAATTCTGCA-ATA
1 AAAATAATTCTGAAGATA
79661 AAAA
1 AAAA
79665 GAGAAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (18 bp):
AAAATAATTCTGAAGATA
Found at i:81278 original size:88 final size:88
Alignment explanation
Indices: 81129--81307 Score: 331
Period size: 88 Copynumber: 2.0 Consensus size: 88
81119 ACTCTTGCTT
*
81129 AATCATCCTGATCAGGGAGTAAACACGATGGTAGATGAAAAGAGCAAAAGGACCAAAATTGATGT
1 AATCATCCTGATCAGGGAGTAAACACGATAGTAGATGAAAAGAGCAAAAGGACCAAAATTGATGT
*
81194 TGGAGAGATCTAATCTCTATTAA
66 TGGAGAGATCTAATCTCCATTAA
*
81217 AATCATCCTGATCAGGGAGTAAACACGATAGTAGATGAAAAGAGCAAAAGGTCCAAAATTGATGT
1 AATCATCCTGATCAGGGAGTAAACACGATAGTAGATGAAAAGAGCAAAAGGACCAAAATTGATGT
81282 TGGAGAGATCTAATCTCCATTAA
66 TGGAGAGATCTAATCTCCATTAA
81305 AAT
1 AAT
81308 GGATCTAGCG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.23
Consensus pattern (88 bp):
AATCATCCTGATCAGGGAGTAAACACGATAGTAGATGAAAAGAGCAAAAGGACCAAAATTGATGT
TGGAGAGATCTAATCTCCATTAA
Found at i:94513 original size:63 final size:63
Alignment explanation
Indices: 94434--94559 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
94424 TTTCGATATA
* *
94434 GTCTTTTAATGTTTGATACTTATATGTT-ATTCTTTCCTTCCGTCAAGATATCTCAGATAAGTT
1 GTCTTTTAATGTTTGATACTTATAT-TTCATTATTTCCTTCCATCAAGATATCTCAGATAAGTT
* *
94497 GTCTTTTAGTGTTTGATACTTATATTTCATTATTTCCTTCCATCAATATATCTCAGATAAGTT
1 GTCTTTTAATGTTTGATACTTATATTTCATTATTTCCTTCCATCAAGATATCTCAGATAAGTT
94560 AAAAGGTGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
62 2 0.03
63 56 0.97
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (63 bp):
GTCTTTTAATGTTTGATACTTATATTTCATTATTTCCTTCCATCAAGATATCTCAGATAAGTT
Found at i:97966 original size:6 final size:6
Alignment explanation
Indices: 97948--97979 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
97938 CCCACCACTG
97948 CTCTCC C-CTCC CTCTCC CTCTCC CTCTCC CTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTC
97980 ATCCTCACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CTCTCC
Found at i:103275 original size:18 final size:18
Alignment explanation
Indices: 103238--103276 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
103228 TAACTTAACC
* **
103238 TTTCATTTTTTTCCTCAT
1 TTTCATTTTTATCCAAAT
103256 TTTCATTTTTATCCAAAT
1 TTTCATTTTTATCCAAAT
103274 TTT
1 TTT
103277 TTAAATTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTCATTTTTATCCAAAT
Found at i:109761 original size:188 final size:189
Alignment explanation
Indices: 109444--109804 Score: 616
Period size: 188 Copynumber: 1.9 Consensus size: 189
109434 CTGTTTTCCC
*
109444 AGTGGTTCTTCTTTATCAAGCTTTCTATGATTTGTAAATGAGATTTAACCAGAGTTATCTCACAT
1 AGTGGTTCTTATTTATCAAGCTTTCTATGATTTGTAAATGAGATTTAACCAGAGTTATCTCACAT
**
109509 TATTGCAGCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGTATGAGCAGGCATGTGGTT-G
66 TATTGCAGCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGTATGAGCAGGCAAATGGTTGG
* * *
109573 GGTGTACATTTGTTACCTCTGCATGTGTGAATGAGTTTTGTTGGCTTTGTGGTTGTCCT
131 GGTGTACACTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTGGCTTTGTGGTTGTCCT
* * *
109632 AGTGGTTCTTATTTATCAAGCTTTCTATGATTTTTAAATGAGCTTTAATCAGAGTTATCTCACAT
1 AGTGGTTCTTATTTATCAAGCTTTCTATGATTTGTAAATGAGATTTAACCAGAGTTATCTCACAT
* *
109697 TATTGCAGCAAATTTCTTCCTATGTATTTTTGGGTTTATTTTTGTATGAGCATGCAAATGGTTGG
66 TATTGCAGCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGTATGAGCAGGCAAATGGTTGG
109762 GGTGTACACTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
131 GGTGTACACTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTG
109805 CTCAGTTTTT
Statistics
Matches: 161, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
188 120 0.75
189 41 0.25
ACGTcount: A:0.22, C:0.13, G:0.21, T:0.44
Consensus pattern (189 bp):
AGTGGTTCTTATTTATCAAGCTTTCTATGATTTGTAAATGAGATTTAACCAGAGTTATCTCACAT
TATTGCAGCAAATTTCTTCCTATATATTTTTGGGTTTATTTTTGTATGAGCAGGCAAATGGTTGG
GGTGTACACTTGCTACCTCTGCATGTGTGAATAAGTTTTGTTGGCTTTGTGGTTGTCCT
Found at i:111561 original size:44 final size:44
Alignment explanation
Indices: 111501--111587 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
111491 TAAAATTGAC
* *
111501 TTTTTACATGATATCTCTTTTTTTAATAAGTTGCTGACTTATTT
1 TTTTTACACGATATCTCTTTTTTAAATAAGTTGCTGACTTATTT
*
111545 TTTTTACACGATATCTCTTTTTTAAATACGTTGCTGACTTATT
1 TTTTTACACGATATCTCTTTTTTAAATAAGTTGCTGACTTATT
111588 ATGTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.54
Consensus pattern (44 bp):
TTTTTACACGATATCTCTTTTTTAAATAAGTTGCTGACTTATTT
Done.