Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000273.1 Hibiscus syriacus cultivar Beakdansim tig00000507_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 127352
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5040 original size:21 final size:19
Alignment explanation
Indices: 5012--5057 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
5002 TCATTGAATC
5012 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
5032 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
5051 ACTTAGT
1 A-TTAGT
5058 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:6606 original size:21 final size:21
Alignment explanation
Indices: 6577--6619 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6567 TTATCCTTGC
6577 AAGAATTCATGGCCTCGACAA
1 AAGAATTCATGGCCTCGACAA
* * *
6598 AAGATTTCATGGCGTCTACAA
1 AAGAATTCATGGCCTCGACAA
6619 A
1 A
6620 GACCTTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (21 bp):
AAGAATTCATGGCCTCGACAA
Found at i:20386 original size:541 final size:541
Alignment explanation
Indices: 19364--20449 Score: 2046
Period size: 541 Copynumber: 2.0 Consensus size: 541
19354 TAGAGCCACG
19364 CCCAACACCTCAGCTGTACCACCTCATCGACCAATAACTCCAGCCCATCCCGTAGCAATGTCGTA
1 CCCAACACCTCAGCTGTACCACCTCATCGACCAATAACTCCAGCCCATCCCGTAGCAATGTCGTA
* *
19429 GGAGTCCTGACTAGAGAGGCTTCGTAGATACACGACCACTGACTTTTTTGGTTCAGGGGATGACG
66 GGAATCCTGACTAGAGAGGCTTCGTAGATACACGACCACTGACTTTTTTGGTTCAGGGGATGACA
*
19494 ATCTCATAGCAGTAGACCAGTGGCTTAGGGAGACTCTGGCAGTTGTATCATACCCCATAAGGTAA
131 ATCTCATAGCAGTAGACCAGTGGCTTAGGGAGACTCTAGCAGTTGTATCATACCCCATAAGGTAA
*
19559 GCTCGAGTTCATCACCACCCTACTCAAGGGTGACACCATTGATTCGTGGGAGACGATAGAGCTGA
196 GCTCGAGTTCATCACCACCCTACTCAAGGGTGACACCATTGATTCATGGGAGACGATAGAGCTGA
*
19624 CATTGGAGCCAGAGAGGTCGACTTAGGAGATGTTCTTATTAGAATTCAGACAGAAATACATCGGT
261 CATTGGAGCCAGAGAGGTCGACTTAGAAGATGTTCTTATTAGAATTCAGACAGAAATACATCGGT
*
19689 GAGGCTTACACCAATGACTTGAGGGAACAATACCTACACTTGACTCAGGGGGATTGTAACATGAT
326 GAGGCTTACACCAATGACTTGAGGGAACAATACCTACACTTAACTCAGGGGGATTGTAACATGAT
* *
19754 AGCGTATGAGAATGAGTTCCTCAGACTGAGTAGGTAAGCTCTAGAGTTGGCCTCGATTGAGGAGC
391 AGAGTATGAGAAAGAGTTCCTCAGACTGAGTAGGTAAGCTCTAGAGTTGGCCTCGATTGAGGAGC
*
19819 ACCATTTCCGTAGGTTCAGAGAAGGCATACACATTGACATCCTATCATACCTTGCAGTTAACCTT
456 ACCATTTCCGTAGGTTCAGAGAAGGCATACACATTGACATCCTATCATACCTTGCAGTTAACCTC
19884 CCAGGGTCTTTGATGAGTTGT
521 CCAGGGTCTTTGATGAGTTGT
*
19905 CCCAACACCTCAGCTGTACCACCTCATCGACCAATACCTCCAGCCCATCCCGTAGCAATGTCGTA
1 CCCAACACCTCAGCTGTACCACCTCATCGACCAATAACTCCAGCCCATCCCGTAGCAATGTCGTA
*
19970 GGAATCCTGACTAGAGAGGCTTCGTAGATACACGACCATTGACTTTTTTGGTTCAGGGGATGACA
66 GGAATCCTGACTAGAGAGGCTTCGTAGATACACGACCACTGACTTTTTTGGTTCAGGGGATGACA
20035 ATCTCATAGCAGTAGACCAGTGGCTTAGGGAGACTCTAGCAGTTGTATCATACCCCATAAGGTAA
131 ATCTCATAGCAGTAGACCAGTGGCTTAGGGAGACTCTAGCAGTTGTATCATACCCCATAAGGTAA
20100 GCTCGAGTTCATCACCACCCTACTCAAGGGTGACACCATTGATTCATGGGAGACGATAGAGCTGA
196 GCTCGAGTTCATCACCACCCTACTCAAGGGTGACACCATTGATTCATGGGAGACGATAGAGCTGA
20165 CATTGGAGCCAGAGAGGTCGACTTAGAAGATGTTCTTATTAGAATTCAGACAGAAATACATCGGT
261 CATTGGAGCCAGAGAGGTCGACTTAGAAGATGTTCTTATTAGAATTCAGACAGAAATACATCGGT
*
20230 GAGGCTTACACCAATGACTTGAGGGAACAATTCCTACACTTAACTCAGGGGGATTGTAACATGAT
326 GAGGCTTACACCAATGACTTGAGGGAACAATACCTACACTTAACTCAGGGGGATTGTAACATGAT
20295 AGAGTATGAGAAAGAGTTCCTCAGACTGAGTAGGTAAGCTCTAGAGTTGGCCTCGATTGAGGAGC
391 AGAGTATGAGAAAGAGTTCCTCAGACTGAGTAGGTAAGCTCTAGAGTTGGCCTCGATTGAGGAGC
* *
20360 ACCATTTTCGTAGGTTCAGAGAAGGCATACACATTGACATCCTATCGTACCTTGCAGTTAACCTC
456 ACCATTTCCGTAGGTTCAGAGAAGGCATACACATTGACATCCTATCATACCTTGCAGTTAACCTC
20425 CCAGGGTCTTTGATGAGTTGT
521 CCAGGGTCTTTGATGAGTTGT
20446 CCCA
1 CCCA
20450 CCAGGCAAAG
Statistics
Matches: 531, Mismatches: 14, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
541 531 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (541 bp):
CCCAACACCTCAGCTGTACCACCTCATCGACCAATAACTCCAGCCCATCCCGTAGCAATGTCGTA
GGAATCCTGACTAGAGAGGCTTCGTAGATACACGACCACTGACTTTTTTGGTTCAGGGGATGACA
ATCTCATAGCAGTAGACCAGTGGCTTAGGGAGACTCTAGCAGTTGTATCATACCCCATAAGGTAA
GCTCGAGTTCATCACCACCCTACTCAAGGGTGACACCATTGATTCATGGGAGACGATAGAGCTGA
CATTGGAGCCAGAGAGGTCGACTTAGAAGATGTTCTTATTAGAATTCAGACAGAAATACATCGGT
GAGGCTTACACCAATGACTTGAGGGAACAATACCTACACTTAACTCAGGGGGATTGTAACATGAT
AGAGTATGAGAAAGAGTTCCTCAGACTGAGTAGGTAAGCTCTAGAGTTGGCCTCGATTGAGGAGC
ACCATTTCCGTAGGTTCAGAGAAGGCATACACATTGACATCCTATCATACCTTGCAGTTAACCTC
CCAGGGTCTTTGATGAGTTGT
Found at i:42239 original size:99 final size:100
Alignment explanation
Indices: 42128--42364 Score: 343
Period size: 101 Copynumber: 2.4 Consensus size: 100
42118 AAAGATAAAT
* * *
42128 TTTATCACTTGAGATGGTTTTTCTTAAAATCAATTTC-ATCTTTTTGAAGTAG-TTCCTCTTGGA
1 TTTATCAATTGAGATGATTTTTCTTAAAATCAATTTCAATCTTTTTGAAATAGTTTCC-CTTGGA
* **
42191 ACACATATTTTGAAATTTTTTCACTCAAAACAAAAA
65 ACACAGATTTTGAAATCATTTCACTCAAAACAAAAA
* *
42227 TTTATCATTTGAGATGATTTTTCTTAAAATCAATTTCATATTTTTTTGAAATAGTTTCCCTTGGA
1 TTTATCAATTGAGATGATTTTTCTTAAAATCAATTTCA-ATCTTTTTGAAATAGTTTCCCTTGGA
*
42292 ACACAGATTTTGAAATCATTTCACTCAAAACCAAAA
65 ACACAGATTTTGAAATCATTTCACTCAAAACAAAAA
*
42328 TTTATCAATTGAGATGTTTTTTTCTTAAAATCAATTT
1 TTTATCAATTGAGATG-ATTTTTCTTAAAATCAATTT
42365 TTCATGAGAT
Statistics
Matches: 124, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
99 35 0.28
101 66 0.53
102 23 0.19
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (100 bp):
TTTATCAATTGAGATGATTTTTCTTAAAATCAATTTCAATCTTTTTGAAATAGTTTCCCTTGGAA
CACAGATTTTGAAATCATTTCACTCAAAACAAAAA
Found at i:43070 original size:139 final size:138
Alignment explanation
Indices: 42701--43097 Score: 535
Period size: 138 Copynumber: 2.9 Consensus size: 138
42691 AGAGAGGATA
* * * * *
42701 AAGCAGTCAACATTTATAGTGGATAGTTCATAATGAGAAGAATGCATCCGATGAGGGAGAATAAG
1 AAGCGGTCAACATTT-CAGTGGAGAGTTCATAATGAGAAGAATTCATCCGATGAGGGAGAAAAAG
* *
42766 TTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAAC
65 TTCATAATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGGAGTTAAATCAGCAAC
42831 ACCTCACTC
130 ACCTCACTC
* * * * *
42840 GAGCGGCCAACATTTCAGTGGAGAGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAAGAAGT
1 AAGCGGTCAACATTTCAGTGGAGAGTTCATAATGAGAAGAATTCATCCGATGAGGGAGAAAAAGT
* * * *
42905 TCATAATGAGAATATCTTGTTCAACCTTAACTTGATTCATCACATATGGAGTTAAATCAGCAATA
66 TCATAATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGGAGTTAAATCAGCAACA
*
42970 TCTCACTC
131 CCTCACTC
* *
42978 AAG-GGATCAACATTTCCAGTGGAGAGTTCATTATGAGAAGAATTCATCCGATAAGGGAGAAAAA
1 AAGCGG-TCAACATTT-CAGTGGAGAGTTCATAATGAGAAGAATTCATCCGATGAGGGAGAAAAA
* * * * *
43042 GTTCATAATGAAAAGAACTTGTTTAACCTTAGCTTGTTTTCATCGCATAAGGAGTT
64 GTTCATAATGAGAAGAACTTGTTCAACCTTAGCTTG-ATTCATCACATATGGAGTT
43098 GGAACAACAC
Statistics
Matches: 224, Mismatches: 31, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
137 2 0.01
138 120 0.54
139 86 0.38
140 16 0.07
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (138 bp):
AAGCGGTCAACATTTCAGTGGAGAGTTCATAATGAGAAGAATTCATCCGATGAGGGAGAAAAAGT
TCATAATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGGAGTTAAATCAGCAACA
CCTCACTC
Found at i:52051 original size:26 final size:25
Alignment explanation
Indices: 52018--52067 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
52008 TATTAGGGAT
52018 TTTATTATTTCAAATT-AATTAAATC
1 TTTATTATTT-AAATTAAATTAAATC
*
52043 TTTATTTATTTAATTTAAATTAAAT
1 TTTA-TTATTTAAATTAAATTAAAT
52068 ATTTGGGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTATTATTTAAATTAAATTAAATC
Found at i:54886 original size:17 final size:17
Alignment explanation
Indices: 54852--54893 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
54842 CCCTTCCCTT
54852 TCTTT-GAGAGAAATTC
1 TCTTTCGAGAGAAATTC
54868 TCTTTCGAGA-AAATCTC
1 TCTTTCGAGAGAAAT-TC
*
54885 TCGTTCGAG
1 TCTTTCGAG
54894 CAACAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (17 bp):
TCTTTCGAGAGAAATTC
Found at i:60135 original size:21 final size:21
Alignment explanation
Indices: 60092--60163 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
60082 GAGTCATGGA
* * * *
60092 AGCTAGCTAGTGGAGTTAGCT
1 AGCTAGGTAGTGTAGATAACT
*
60113 AGCTAGGTAGCT-TAGGTAACT
1 AGCTAGGTAG-TGTAGATAACT
60134 AGCTAGGTAGTGTAGATAACT
1 AGCTAGGTAGTGTAGATAACT
60155 AGCTAGGTA
1 AGCTAGGTA
60164 CCTAGTGACA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
20 1 0.02
21 42 0.95
22 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.31, T:0.28
Consensus pattern (21 bp):
AGCTAGGTAGTGTAGATAACT
Found at i:60532 original size:30 final size:30
Alignment explanation
Indices: 60498--60567 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
60488 CTATGATGCA
*
60498 AATGAGCTAATTATAAATGCATAAACATGG
1 AATGAGCTAATTATAAATGCATAAACATAG
*
60528 AATGAGCTAATTATGAATGCATAAACATAG
1 AATGAGCTAATTATAAATGCATAAACATAG
*
60558 AAAGAGCTAA
1 AATGAGCTAA
60568 AGAATGATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (30 bp):
AATGAGCTAATTATAAATGCATAAACATAG
Found at i:60578 original size:30 final size:30
Alignment explanation
Indices: 60513--60586 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
60503 GCTAATTATA
* * **
60513 AATGCATAAACATGGAATGAGCTAATTATG
1 AATGCATAAACATAGAAAGAGCTAAGAATG
60543 AATGCATAAACATAGAAAGAGCTAAAGAATG
1 AATGCATAAACATAGAAAGAGCT-AAGAATG
60574 -ATGCATAAACATA
1 AATGCATAAACATA
60587 TAATAAAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 34 0.87
31 5 0.13
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.22
Consensus pattern (30 bp):
AATGCATAAACATAGAAAGAGCTAAGAATG
Found at i:60981 original size:39 final size:39
Alignment explanation
Indices: 60938--61014 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
60928 AGCAAGATGA
60938 AGAGTATAAGGTGTAAGAGTAGGATCACATCACCACACG
1 AGAGTATAAGGTGTAAGAGTAGGATCACATCACCACACG
60977 AGAGTATAAGGTGTAAGAGTAGGATCACATCACCACAC
1 AGAGTATAAGGTGTAAGAGTAGGATCACATCACCACAC
61015 CAATTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (39 bp):
AGAGTATAAGGTGTAAGAGTAGGATCACATCACCACACG
Found at i:69050 original size:60 final size:60
Alignment explanation
Indices: 68941--69078 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
68931 TAATTAAATG
* *** * * *
68941 ATCATTTTATAATTTTTAATAGTTAAAGGATTTAACAAAGTAGTTTCTTATAGTTAGGGG
1 ATCATTTTATAATTTTTAATAGTCAAAGGATTTAACAAAGTAAAGTCTTATAATCAGGGA
* *
69001 ATTATTTTATAATTTTTAATAGTC-AAGAGATTTAACAATGTAAAGTCTTATAATCAGGGA
1 ATCATTTTATAATTTTTAATAGTCAAAG-GATTTAACAAAGTAAAGTCTTATAATCAGGGA
69061 ATCATTTCTAT-ATTTTTA
1 ATCATTT-TATAATTTTTA
69079 CCCATATTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
59 3 0.05
60 60 0.91
61 3 0.05
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (60 bp):
ATCATTTTATAATTTTTAATAGTCAAAGGATTTAACAAAGTAAAGTCTTATAATCAGGGA
Found at i:69548 original size:10 final size:10
Alignment explanation
Indices: 69529--69591 Score: 67
Period size: 10 Copynumber: 6.2 Consensus size: 10
69519 ATGGAAGAAT
69529 AATA-AAATA
1 AATATAAATA
69538 AATATAAATA
1 AATATAAATA
*
69548 AATATAAACA
1 AATATAAATA
69558 AA-ATAAATAA
1 AATATAAAT-A
69568 AATAGTAAAATA
1 AATA-T-AAATA
*
69580 AATAAAAATA
1 AATATAAATA
69590 AA
1 AA
69592 AAAAGAAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
9 9 0.20
10 26 0.57
11 1 0.02
12 6 0.13
13 4 0.09
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (10 bp):
AATATAAATA
Found at i:69670 original size:11 final size:12
Alignment explanation
Indices: 69579--69670 Score: 53
Period size: 12 Copynumber: 7.2 Consensus size: 12
69569 ATAGTAAAAT
*
69579 AAATAAAAATAA
1 AAATAAAAACAA
* *
69591 AAAAAGAAAAGAA
1 AAATA-AAAACAA
69604 AAATAAAAACAA
1 AAATAAAAACAA
* *
69616 AGGA-AAAAATAA
1 A-AATAAAAACAA
*
69628 TGAAATTAAATAGAAAA
1 --AAA-TAAA-A-ACAA
69645 AAATAAAAACAA
1 AAATAAAAACAA
69657 AAAT-AAAACAA
1 AAATAAAAACAA
69668 AAA
1 AAA
69671 GAGAGAAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
11 10 0.16
12 25 0.40
13 13 0.21
14 5 0.08
15 6 0.10
16 1 0.02
17 3 0.05
ACGTcount: A:0.79, C:0.03, G:0.07, T:0.11
Consensus pattern (12 bp):
AAATAAAAACAA
Found at i:69688 original size:11 final size:11
Alignment explanation
Indices: 69574--69696 Score: 67
Period size: 11 Copynumber: 10.9 Consensus size: 11
69564 ATAAAATAGT
69574 AAAATAAATAA-
1 AAAA-AAATAAG
*
69585 AAATAAAAAAAG
1 AAA-AAAATAAG
*
69597 AAAAGAAA-AAT
1 AAAA-AAATAAG
*
69608 AAAAACA-AAG
1 AAAAAAATAAG
*
69618 GAAAAAATAATG
1 AAAAAAATAA-G
*
69630 AAATTAAAT-AG
1 AAA-AAAATAAG
*
69641 AAAAAAATAAA
1 AAAAAAATAAG
69652 AACAAAAATAA-
1 AA-AAAAATAAG
*
69663 AACAAAAAGAGAG
1 AA-AAAAATA-AG
69676 AAAAAAATAAG
1 AAAAAAATAAG
*
69687 AATAAAATAA
1 AAAAAAATAA
69697 TATATATATA
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
10 13 0.15
11 44 0.49
12 26 0.29
13 6 0.07
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.11
Consensus pattern (11 bp):
AAAAAAATAAG
Found at i:72345 original size:60 final size:60
Alignment explanation
Indices: 72271--72421 Score: 187
Period size: 60 Copynumber: 2.5 Consensus size: 60
72261 CATATTTGAT
* * * *
72271 TTAAAGGA-TCAAAATAGAAAAAATAGAAATTTAAAGGACTAAAATAGCAAATACAAAAAA
1 TTAAAGGACT-AAAATAGAAAATATAGAAATTTAAAAGACGAAAATAGCAAAAACAAAAAA
* * * * *
72331 TTAAAGGACTAAAATATAAAATACATAAACTTAAAAGACGAAAATAGCAAAAACAAAAAT
1 TTAAAGGACTAAAATAGAAAATATAGAAATTTAAAAGACGAAAATAGCAAAAACAAAAAA
* *
72391 TTTAAGGACTAAAATAGCAAATATAGAAATT
1 TTAAAGGACTAAAATAGAAAATATAGAAATT
72422 CAGAGGGATG
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 74 0.99
61 1 0.01
ACGTcount: A:0.61, C:0.08, G:0.11, T:0.21
Consensus pattern (60 bp):
TTAAAGGACTAAAATAGAAAATATAGAAATTTAAAAGACGAAAATAGCAAAAACAAAAAA
Found at i:72421 original size:30 final size:30
Alignment explanation
Indices: 72269--72413 Score: 157
Period size: 30 Copynumber: 4.8 Consensus size: 30
72259 ATCATATTTG
* * * *
72269 ATTTAAAGGA-TCAAAATAGAAAAAATAGAA
1 ATTTAAAGGACT-AAAATAGCAAATACAAAA
72299 ATTTAAAGGACTAAAATAGCAAATACAAAA
1 ATTTAAAGGACTAAAATAGCAAATACAAAA
* ** *
72329 AATTAAAGGACTAAAATATAAAATACATAA
1 ATTTAAAGGACTAAAATAGCAAATACAAAA
* * * *
72359 ACTTAAAAGACGAAAATAGCAAAAACAAAA
1 ATTTAAAGGACTAAAATAGCAAATACAAAA
*
72389 ATTTTAAGGACTAAAATAGCAAATA
1 ATTTAAAGGACTAAAATAGCAAATA
72414 TAGAAATTCA
Statistics
Matches: 94, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
30 93 0.99
31 1 0.01
ACGTcount: A:0.61, C:0.08, G:0.10, T:0.20
Consensus pattern (30 bp):
ATTTAAAGGACTAAAATAGCAAATACAAAA
Found at i:73623 original size:16 final size:16
Alignment explanation
Indices: 73602--73646 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
73592 CCTAGGTGAG
*
73602 TCGGGTCGAATCTGGT
1 TCGGGTCGGATCTGGT
* *
73618 TCGGGTTGGATCGGGT
1 TCGGGTCGGATCTGGT
*
73634 TCAGGTCGGATCT
1 TCGGGTCGGATCT
73647 TGGGCTTCCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.11, C:0.18, G:0.40, T:0.31
Consensus pattern (16 bp):
TCGGGTCGGATCTGGT
Found at i:73786 original size:3 final size:3
Alignment explanation
Indices: 73778--73813 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
73768 GTACATTAAT
*
73778 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
73814 TATTTTTTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:74181 original size:51 final size:51
Alignment explanation
Indices: 74053--74167 Score: 221
Period size: 51 Copynumber: 2.3 Consensus size: 51
74043 TCGGTGGATG
74053 ACACGGTTCCTACATGAAGAGGACGGCATGCCATCTTTAGGAAGGGTGATA
1 ACACGGTTCCTACATGAAGAGGACGGCATGCCATCTTTAGGAAGGGTGATA
*
74104 ACACGGTTCCTATATGAAGAGGACGGCATGCCATCTTTAGGAAGGGTGATA
1 ACACGGTTCCTACATGAAGAGGACGGCATGCCATCTTTAGGAAGGGTGATA
74155 ACACGGTTCCTAC
1 ACACGGTTCCTAC
74168 GCTATGAGGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.23
Consensus pattern (51 bp):
ACACGGTTCCTACATGAAGAGGACGGCATGCCATCTTTAGGAAGGGTGATA
Found at i:74300 original size:43 final size:43
Alignment explanation
Indices: 74155--74303 Score: 141
Period size: 43 Copynumber: 3.5 Consensus size: 43
74145 AAGGGTGATA
* *
74155 ACACGGTTCCTACGCT-ATGAGGACGGCTGGTTATCTAGGGGTG
1 ACACGGTTCCTACG-TGATGAGGACGGTTGGTTATCCAGGGGTG
*
74198 ACACGGCTCCTACGTGATGAGGA-GTGTTGG---T-CAGGGGATG
1 ACACGGTTCCTACGTGATGAGGACG-GTTGGTTATCCAGGGG-TG
* * * **
74238 ATACTGTTCCTACATGATGAGGACGGTTGGTTATCCAAAGGTG
1 ACACGGTTCCTACGTGATGAGGACGGTTGGTTATCCAGGGGTG
74281 ACACGGCTT-CTACGTGATGAGGA
1 ACACGG-TTCCTACGTGATGAGGA
74304 GGTCTAGTCG
Statistics
Matches: 85, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
39 5 0.06
40 27 0.32
41 1 0.01
42 2 0.02
43 44 0.52
44 6 0.07
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.26
Consensus pattern (43 bp):
ACACGGTTCCTACGTGATGAGGACGGTTGGTTATCCAGGGGTG
Found at i:74399 original size:130 final size:131
Alignment explanation
Indices: 74243--74621 Score: 471
Period size: 130 Copynumber: 2.9 Consensus size: 131
74233 GGATGATACT
*
74243 GTTCCTACATGATGAGGACGGTTGGTTATCCAAAGGTGACACGGCTTCTACGTGATGAGGAGGTC
1 GTTCCTACATGATGAGGATGGTTGGTTATCCAAAGGTGACACGGCTTCTACGTGATGAGGAGGTC
* * *
74308 TAGTCGG-GGATGACACGATTCCTATGCAATGGGGA-TGGTAAGCCATCTTTAGGGATGATAACA
66 TAGTCGGTGGATGACACGGTTCCTACGCAATGAGGACT-GTAAGCCATCTTTAGGGATGATAACA
74371 CG
130 CG
* * * * * * ** * *
74373 GTTCCTACGTAATGAGGATGGCTGGTTAT-CTATGGTAACACAAC-TCTTACGTGATGAGAAGTT
1 GTTCCTACATGATGAGGATGGTTGGTTATCCAAAGGTGACACGGCTTC-TACGTGATGAGGAGGT
* *
74436 CTGGTCGGTGGATGACACGGTTCCTACGCGATGAGGACTGTAAGCCATCTTTAGGGATGATAACA
65 CTAGTCGGTGGATGACACGGTTCCTACGCAATGAGGACTGTAAGCCATCTTTAGGGATGATAACA
74501 CG
130 CG
* ** * * *
74503 GTTCCTACATGATGAGGATGGTTGGTTATCTATGGGTGACATGGCTCCTACGTGATGACGAGGTC
1 GTTCCTACATGATGAGGATGGTTGGTTATCCAAAGGTGACACGGCTTCTACGTGATGAGGAGGTC
* * *
74568 TAGTCGGTGGATGACACGGTTCCTACGCGATGAGGACGGCATA-CCATCTTTAGG
66 TAGTCGGTGGATGACACGGTTCCTACGCAATGAGGACTGTA-AGCCATCTTTAGG
74622 ATAATGGTTT
Statistics
Matches: 209, Mismatches: 34, Indels: 11
0.82 0.13 0.04
Matches are distributed among these distances:
128 2 0.01
129 31 0.15
130 103 0.49
131 71 0.34
132 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (131 bp):
GTTCCTACATGATGAGGATGGTTGGTTATCCAAAGGTGACACGGCTTCTACGTGATGAGGAGGTC
TAGTCGGTGGATGACACGGTTCCTACGCAATGAGGACTGTAAGCCATCTTTAGGGATGATAACAC
G
Found at i:74826 original size:65 final size:66
Alignment explanation
Indices: 74628--74849 Score: 222
Period size: 65 Copynumber: 3.4 Consensus size: 66
74618 TAGGATAATG
* * * * * *
74628 GTTTCAAGAGAAACCGACTCACAGAT-GATGCTTT-AAGAGAATCTATCTCAAGAGAGACAAAAT
1 GTTTCAAGGGAAACAGTCTCAAAGATGGATG-TTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
74691 TT
65 TT
* * * * *
74693 GTTTAAAGGGAAAC-GATATCAAAGATGGGTGTTTCAAGAGAAACTTTCTCAAGGGAGAC-AAAT
1 GTTTCAAGGGAAACAG-TCTCAAAGATGGATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
74756 CTT
65 -TT
* *
74759 GTTTCAAGGGAAACAGTCTCAAAGGT-GATGTTTCATA-AGAAACTGTCTCGAGAGAGACAAAAT
1 GTTTCAAGGGAAACAGTCTCAAAGATGGATGTTTCA-AGAGAAACTGTCTCAAGAGAGACAAAAT
74822 TT
65 TT
* * *
74824 GTTTCAAGAGAAATAGACTCAAAGAT
1 GTTTCAAGGGAAACAGTCTCAAAGAT
74850 TATAAATTTT
Statistics
Matches: 130, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
64 1 0.01
65 76 0.58
66 52 0.40
67 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (66 bp):
GTTTCAAGGGAAACAGTCTCAAAGATGGATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
T
Found at i:75054 original size:37 final size:35
Alignment explanation
Indices: 74897--75057 Score: 105
Period size: 37 Copynumber: 4.5 Consensus size: 35
74887 GTTTTTTAAA
* * *
74897 TAAATAAATT-TCTCAAGCGAGACGACATTTATTTT
1 TAAAAAAATTGTCTCAAGCGAGACAAAATTT-TTTT
* * * ****
74932 GAGAGAAATTGTCTCAAGCGAGACAAAA-AAAATT
1 TAAAAAAATTGTCTCAAGCGAGACAAAATTTTTTT
*
74966 TAGAAAAAGATT-TCTCAAGCGAGA-TAAATTTTTTAT
1 TA-AAAAA-ATTGTCTCAAGCGAGACAAAATTTTTT-T
* *
75002 ATATATAAAACTGTCTCAAGCGAGACAAAATTTGTTTT
1 -TA-AAAAAATTGTCTCAAGCGAGACAAAATTT-TTTT
75040 TAAAAGAAATTGTCTCAA
1 TAAAA-AAATTGTCTCAA
75058 AGTCAACAAC
Statistics
Matches: 93, Mismatches: 23, Indels: 18
0.69 0.17 0.13
Matches are distributed among these distances:
34 6 0.06
35 23 0.25
36 23 0.25
37 31 0.33
38 7 0.08
39 3 0.03
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (35 bp):
TAAAAAAATTGTCTCAAGCGAGACAAAATTTTTTT
Found at i:75170 original size:32 final size:32
Alignment explanation
Indices: 75129--75191 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
75119 TTCATTTCAG
*
75129 GATGTTGAATTTCCAAAGATGCCCCAACATTC
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
* *
75161 GATGTTGAATCTCTAAAGATGCCCCATCATT
1 GATGTTGAATCTCCAAAGATGCCCCAACATT
75192 TATCATTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTC
Found at i:76245 original size:16 final size:16
Alignment explanation
Indices: 76226--76275 Score: 68
Period size: 15 Copynumber: 3.1 Consensus size: 16
76216 TTCTTATATA
76226 TTTTTTTTCTTTTGC-
1 TTTTTTTTCTTTTGCT
76241 TTTTTTTTCTCTTTGCT
1 TTTTTTTTCT-TTTGCT
76258 TTTTGTTTTCTTTT-CT
1 TTTT-TTTTCTTTTGCT
76274 TT
1 TT
76276 GCTTTCTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.31
16 9 0.28
17 7 0.22
18 6 0.19
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCTTTTGCT
Found at i:76274 original size:21 final size:23
Alignment explanation
Indices: 76235--76280 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
76225 ATTTTTTTTC
*
76235 TTTTGCTTTTTTTTCTCTTTGCT
1 TTTTGCTTTTCTTTCTCTTTGCT
76258 TTTTG-TTTTCTTT-TCTTTGCT
1 TTTTGCTTTTCTTTCTCTTTGCT
76279 TT
1 TT
76281 CTTTTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 7 0.32
23 5 0.23
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (23 bp):
TTTTGCTTTTCTTTCTCTTTGCT
Found at i:76287 original size:16 final size:15
Alignment explanation
Indices: 76226--76275 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 15
76216 TTCTTATATA
76226 TTTTTTTTCTTTTGCT
1 TTTTTTTTC-TTTGCT
76242 TTTTTTTCTCTTTGCT
1 TTTTTTT-TCTTTGCT
*
76258 TTTTGTTTTCTTTTCT
1 TTTT-TTTTCTTTGCT
76274 TT
1 TT
76276 GCTTTCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 26 0.84
17 5 0.16
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCTTTGCT
Found at i:76287 original size:21 final size:20
Alignment explanation
Indices: 76240--76288 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
76230 TTTTCTTTTG
76240 CTTTTTTTTCTCTTTGCTTT
1 CTTTTTTTTCTCTTTGCTTT
*
76260 -TTGTTTTCTTTTCTTTGCTTT
1 CTT-TTTT-TTCTCTTTGCTTT
76281 CTTTTTTT
1 CTTTTTTT
76289 GTTTTGATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 2 0.08
20 5 0.20
21 16 0.64
22 2 0.08
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (20 bp):
CTTTTTTTTCTCTTTGCTTT
Found at i:79810 original size:30 final size:28
Alignment explanation
Indices: 79756--79840 Score: 97
Period size: 30 Copynumber: 3.0 Consensus size: 28
79746 GTCATATTCG
79756 ATTTAAAGGA-TCAAAATAGCAAAAACATAA
1 ATTTAAAGGACT-AAAATAG-AAAAACA-AA
*
79786 ATTTAAAGGACTAAATTAG-AAAA-AAA
1 ATTTAAAGGACTAAAATAGAAAAACAAA
79812 ATTT-AAGGACTAAAATAGAAAATACAAA
1 ATTTAAAGGACTAAAATAGAAAA-ACAAA
79840 A
1 A
79841 ATTCAGAGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
25 13 0.27
26 9 0.18
27 2 0.04
28 8 0.16
30 16 0.33
31 1 0.02
ACGTcount: A:0.61, C:0.07, G:0.11, T:0.21
Consensus pattern (28 bp):
ATTTAAAGGACTAAAATAGAAAAACAAA
Found at i:79823 original size:25 final size:26
Alignment explanation
Indices: 79756--79833 Score: 88
Period size: 25 Copynumber: 2.9 Consensus size: 26
79746 GTCATATTCG
79756 ATTTAAAGGA-TCAAAATAGCAAAAACATAA
1 ATTTAAAGGACT-AAAATAG--AAAA-A-AA
*
79786 ATTTAAAGGACTAAATTAGAAAAAAA
1 ATTTAAAGGACTAAAATAGAAAAAAA
79812 ATTT-AAGGACTAAAATAGAAAA
1 ATTTAAAGGACTAAAATAGAAAA
79834 TACAAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
25 17 0.38
26 6 0.13
27 1 0.02
28 4 0.09
30 16 0.36
31 1 0.02
ACGTcount: A:0.60, C:0.06, G:0.12, T:0.22
Consensus pattern (26 bp):
ATTTAAAGGACTAAAATAGAAAAAAA
Found at i:85028 original size:31 final size:31
Alignment explanation
Indices: 84990--85109 Score: 127
Period size: 31 Copynumber: 3.8 Consensus size: 31
84980 GTATAATTTT
* * *
84990 TTTTATAAATATAATGATTATTCTATACTAA
1 TTTTATAAATTTAATGATTATTTTATAATAA
* *
85021 TTTTATAAATTTTAATGATCATTTTGTAAT-A
1 TTTTATAAA-TTTAATGATTATTTTATAATAA
*
85052 TTTTAATAAAAATTTAATTATTATTTTATAATAA
1 TTTT-AT--AAATTTAATGATTATTTTATAATAA
*
85086 TTTTATAAATTTAAT-ATTTTTTTA
1 TTTTATAAATTTAATGATTATTTTA
85110 AAAATTAAAT
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
30 8 0.11
31 23 0.31
32 17 0.23
33 19 0.25
34 8 0.11
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (31 bp):
TTTTATAAATTTAATGATTATTTTATAATAA
Found at i:85066 original size:22 final size:21
Alignment explanation
Indices: 85019--85101 Score: 62
Period size: 22 Copynumber: 3.9 Consensus size: 21
85009 ATTCTATACT
* *
85019 AATTTTATAAATTTTAATGAT
1 AATTTTATAAATTTTAATAAA
* *
85040 CATTTTGTAATATTTTAATAAA
1 AATTTTATAA-ATTTTAATAAA
* * *
85062 AATTTAATTATTATTTT-ATAAT
1 AATTTTA-TA-AATTTTAATAAA
85084 AATTTTATAAA-TTTAATA
1 AATTTTATAAATTTTAATA
85102 TTTTTTTAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 9
0.70 0.16 0.13
Matches are distributed among these distances:
19 3 0.06
20 4 0.09
21 10 0.21
22 23 0.49
23 7 0.15
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (21 bp):
AATTTTATAAATTTTAATAAA
Found at i:85078 original size:33 final size:33
Alignment explanation
Indices: 84996--85094 Score: 103
Period size: 33 Copynumber: 3.0 Consensus size: 33
84986 TTTTTTTTAT
* * * *
84996 AAATATAATGATTATTCTATACTAATTTTAT-A
1 AAATTTAATGATCATTTTATAATAATTTTATAA
* *
85028 AATTTTAATGATCATTTTGTAAT-ATTTTAATAA
1 AAATTTAATGATCATTTTATAATAATTTT-ATAA
* *
85061 AAATTTAATTATTATTTTATAATAATTTTATAA
1 AAATTTAATGATCATTTTATAATAATTTTATAA
85094 A
1 A
85095 TTTAATATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
31 5 0.09
32 19 0.35
33 25 0.46
34 5 0.09
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (33 bp):
AAATTTAATGATCATTTTATAATAATTTTATAA
Found at i:85088 original size:11 final size:11
Alignment explanation
Indices: 85013--85093 Score: 51
Period size: 11 Copynumber: 7.5 Consensus size: 11
85003 ATGATTATTC
*
85013 TATACTAATTT
1 TATAATAATTT
85024 TAT-A-AATTT
1 TATAATAATTT
* *
85033 TAATGATCATTT
1 T-ATAATAATTT
*
85045 TGTAAT-ATTT
1 TATAATAATTT
*
85055 TAATAAAAATTT
1 T-ATAATAATTT
* * *
85067 AATTATTATTT
1 TATAATAATTT
85078 TATAATAATTT
1 TATAATAATTT
85089 TATAA
1 TATAA
85094 ATTTAATATT
Statistics
Matches: 52, Mismatches: 13, Indels: 10
0.69 0.17 0.13
Matches are distributed among these distances:
9 6 0.12
10 7 0.13
11 30 0.58
12 9 0.17
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TATAATAATTT
Found at i:87300 original size:34 final size:33
Alignment explanation
Indices: 87194--87322 Score: 122
Period size: 32 Copynumber: 3.9 Consensus size: 33
87184 TAGTCACTAA
* * **
87194 CTTACTAACATTCTAACATTTA-TTTTATCATT
1 CTTACTAACATACTAACTTTTATTTTTATTGTT
** *
87226 CGAACTAACATTCTAACTTTTATTTATT-TT-TT
1 CTTACTAACATACTAACTTTTATTT-TTATTGTT
87258 CTTACTAACATACTAACTTTTTATTTTTATTGTT
1 CTTACTAACATACTAAC-TTTTATTTTTATTGTT
* *
87292 CTTGCTAACTTACTAACATTTTA-TTTTATTG
1 CTTACTAACATACTAAC-TTTTATTTTTATTG
87323 CACAACCTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
32 37 0.45
33 21 0.26
34 24 0.29
ACGTcount: A:0.28, C:0.16, G:0.03, T:0.53
Consensus pattern (33 bp):
CTTACTAACATACTAACTTTTATTTTTATTGTT
Found at i:103310 original size:42 final size:43
Alignment explanation
Indices: 103261--103358 Score: 128
Period size: 42 Copynumber: 2.3 Consensus size: 43
103251 AGGATCAGAT
** ** *
103261 TTATTATTTTATTAGGAATTA-AGGTTGGGTTATTTTTAG-TTA
1 TTATTATTTTATTAGGAATTAGA-GTTAAGACATGTTTAGTTTA
103303 TTATTATTTTATTAGGAATTAGAGTTAAGACATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAGAGTTAAGACATGTTTAGTTTA
103346 TTATTATTTTATT
1 TTATTATTTTATT
103359 CTTTAGTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 32 0.65
43 17 0.35
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.55
Consensus pattern (43 bp):
TTATTATTTTATTAGGAATTAGAGTTAAGACATGTTTAGTTTA
Found at i:103782 original size:11 final size:11
Alignment explanation
Indices: 103768--103798 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
103758 TCTTTTCTTT
103768 ATCTTATTTTA
1 ATCTTATTTTA
*
103779 ATCTTGTTTTA
1 ATCTTATTTTA
103790 ATCTTATTT
1 ATCTTATTT
103799 CTTACCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.03, T:0.65
Consensus pattern (11 bp):
ATCTTATTTTA
Found at i:104186 original size:22 final size:21
Alignment explanation
Indices: 104137--104186 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
104127 AAAAAAAAGG
*
104137 AAAAAAAGGCCAAAAAACAAC
1 AAAAAAAGGCCAAAAAACAAA
*
104158 AAAAAAAGGCCAAAAATTCAAA
1 AAAAAAAGGCCAAAAA-ACAAA
104180 AAAAAAA
1 AAAAAAA
104187 TCAAACGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.74, C:0.14, G:0.08, T:0.04
Consensus pattern (21 bp):
AAAAAAAGGCCAAAAAACAAA
Found at i:115565 original size:32 final size:34
Alignment explanation
Indices: 115494--115622 Score: 126
Period size: 32 Copynumber: 3.9 Consensus size: 34
115484 TAATCACTAA
* **
115494 CTTACTAACATTTTAACA-TTTATTTTA-TCATT
1 CTTACTAACATTCTAACATTTTATTTTATTGGTT
**
115526 CGAACTAACATTCTAAC-TTTTA-TTTATTGGTT
1 CTTACTAACATTCTAACATTTTATTTTATTGGTT
* *
115558 CTTACTAACATACTAACTTTTTATTTTTATT-GTT
1 CTTACTAACATTCTAACATTTTA-TTTTATTGGTT
*
115592 CTTACAAAC-TTACTAACATTTTATTTTATTG
1 CTTACTAACATT-CTAACATTTTATTTTATTG
115623 CACAAACTAA
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
31 4 0.05
32 35 0.44
33 13 0.16
34 21 0.27
35 6 0.08
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (34 bp):
CTTACTAACATTCTAACATTTTATTTTATTGGTT
Found at i:115606 original size:34 final size:33
Alignment explanation
Indices: 115532--115622 Score: 114
Period size: 34 Copynumber: 2.8 Consensus size: 33
115522 CATTCGAACT
* *
115532 AACATTCTAAC-TTTTA-TTTATTGGTTCTTACT
1 AACATACTAACATTTTATTTTATT-GTTCTTACA
*
115564 AACATACTAACTTTTTATTTTTATTGTTCTTACA
1 AACATACTAACATTTTA-TTTTATTGTTCTTACA
*
115598 AACTTACTAACATTTTATTTTATTG
1 AACATACTAACATTTTATTTTATTG
115623 CACAAACTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
32 10 0.19
33 13 0.25
34 23 0.44
35 6 0.12
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (33 bp):
AACATACTAACATTTTATTTTATTGTTCTTACA
Found at i:115627 original size:29 final size:32
Alignment explanation
Indices: 115568--115630 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 32
115558 CTTACTAACA
*
115568 TACTAACTTTTTATTTTTATTGTTCTTACAAACT
1 TACTAACATTTTATTTTTATTG-TC-TACAAACT
115602 TACTAACATTTTA-TTTTATTG-C-ACAAACT
1 TACTAACATTTTATTTTTATTGTCTACAAACT
115631 AACCGCTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 7 0.25
31 1 0.04
33 8 0.29
34 12 0.43
ACGTcount: A:0.30, C:0.16, G:0.03, T:0.51
Consensus pattern (32 bp):
TACTAACATTTTATTTTTATTGTCTACAAACT
Found at i:116356 original size:5 final size:5
Alignment explanation
Indices: 116348--116422 Score: 71
Period size: 5 Copynumber: 14.8 Consensus size: 5
116338 TGTTTTACAT
* * * * *
116348 TTTTA TTTTA TTATT- TTTTA TCTCA TTCTA TTTTTA TTTTA TTTTG TTTTG
1 TTTTA TTTTA TT-TTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA TTTTA
*
116399 TTTTA TTTTG TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT
116423 TATCTTTGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
4 2 0.04
5 49 0.86
6 6 0.11
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:116367 original size:15 final size:14
Alignment explanation
Indices: 116347--116423 Score: 82
Period size: 15 Copynumber: 5.1 Consensus size: 14
116337 TTGTTTTACA
116347 TTTTTATTTTATTAT
1 TTTTTATTTTATT-T
* *
116362 TTTTTATCTCATTCT
1 TTTTTATTTTATT-T
116377 ATTTTTATTTTATTT
1 -TTTTTATTTTATTT
*
116392 TGTTTTGTTTTATTT
1 T-TTTTATTTTATTT
116407 TGTTTTATTTTATTT
1 T-TTTTATTTTATTT
116422 TT
1 TT
116424 ATCTTTGATA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
14 2 0.04
15 40 0.75
16 11 0.21
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (14 bp):
TTTTTATTTTATTT
Done.