Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004810.1 Hibiscus syriacus cultivar Beakdansim tig00010832_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: 90171
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1435 original size:93 final size:91
Alignment explanation
Indices: 1338--1523 Score: 318
Period size: 93 Copynumber: 2.0 Consensus size: 91
1328 TGCGTAAATT
* * *
1338 GTAAACTTATTCACTGAATTTTATTCTATCTCTTATTTTACTCATTATATTTTTAGTTTTTTTTA
1 GTAAACTTATTCACTGAATTTTACTCTATCTCTTATTTTACTCATTATACTTTTA-ATTTTTTT-
1403 AATTTAATCACTCAACTTTATACATTGA
64 AATTTAATCACTCAACTTTATACATTGA
1431 GTAAACTTATTCACTGAATTTTACTCTATCTCTTATTTTACTCATTATACTTTTAATTTTTTTAA
1 GTAAACTTATTCACTGAATTTTACTCTATCTCTTATTTTACTCATTATACTTTTAATTTTTTTAA
*
1496 TTTAATCATTCAACTTTATACATTGA
66 TTTAATCACTCAACTTTATACATTGA
1522 GT
1 GT
1524 TTTTTTGGTT
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
91 29 0.33
92 7 0.08
93 53 0.60
ACGTcount: A:0.29, C:0.15, G:0.04, T:0.52
Consensus pattern (91 bp):
GTAAACTTATTCACTGAATTTTACTCTATCTCTTATTTTACTCATTATACTTTTAATTTTTTTAA
TTTAATCACTCAACTTTATACATTGA
Found at i:5668 original size:18 final size:18
Alignment explanation
Indices: 5645--5717 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
5635 ACTGAATATT
5645 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
5663 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* * *
5682 TTATTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
5701 TGTCCCTAAGGACCACT
1 TGTCCCGAAGGACCACT
5718 GATTATCCCT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 30 0.65
19 2 0.04
20 14 0.30
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:5692 original size:38 final size:38
Alignment explanation
Indices: 5649--5723 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
5639 AATATTTGTC
*
5649 CCGAAGGACCACTATGTCCCGAAGGACCACTGATTATT
1 CCGAAGAACCACTATGTCCCGAAGGACCACTGATTATT
*
5687 CCGAAGAACCACTATGTCCCTAAGGACCACTGATTAT
1 CCGAAGAACCACTATGTCCCGAAGGACCACTGATTAT
5724 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (38 bp):
CCGAAGAACCACTATGTCCCGAAGGACCACTGATTATT
Found at i:5970 original size:2 final size:2
Alignment explanation
Indices: 5963--6000 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5953 ATTGTATCCA
5963 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6001 GGATGCATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6404 original size:19 final size:19
Alignment explanation
Indices: 6380--6431 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
6370 TTTAAGCAGG
*
6380 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCGTA
*
6399 TGCATCGATACACTCCGTA
1 TGCATCGATGCACTCCGTA
6418 TGCATCGATGCACT
1 TGCATCGATGCACT
6432 AATTGCATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (19 bp):
TGCATCGATGCACTCCGTA
Found at i:7493 original size:29 final size:28
Alignment explanation
Indices: 7452--7523 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 28
7442 GCTGGCAATG
* *
7452 AACCGACTGAAAACTGGTAGAACCGGTTGAA
1 AACCGA-T-AAAACGGGT-GAACCGGCTGAA
7483 AACCGATAAAACCGGGTGAACCGGCTGAA
1 AACCGATAAAA-CGGGTGAACCGGCTGAA
*
7512 AACCGACAAAAC
1 AACCGATAAAAC
7524 CGATTTGAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.03
29 25 0.68
30 5 0.14
31 6 0.16
ACGTcount: A:0.42, C:0.24, G:0.24, T:0.11
Consensus pattern (28 bp):
AACCGATAAAACGGGTGAACCGGCTGAA
Found at i:7798 original size:24 final size:25
Alignment explanation
Indices: 7756--7802 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
7746 AAACTCAAAA
*
7756 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAGAAGTTCAATTGAAGCCT
*
7781 AAAATTTG-AGTTCAATTGAAGC
1 AAAATTAGAAGTTCAATTGAAGC
7803 GAAAGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (25 bp):
AAAATTAGAAGTTCAATTGAAGCCT
Found at i:8751 original size:16 final size:16
Alignment explanation
Indices: 8698--8739 Score: 75
Period size: 17 Copynumber: 2.6 Consensus size: 16
8688 ATCTCAGAAT
8698 ATCAAACGACTATATA
1 ATCAAACGACTATATA
8714 ATCCAAACGACTATATA
1 AT-CAAACGACTATATA
8731 ATCAAACGA
1 ATCAAACGA
8740 TTATGAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (16 bp):
ATCAAACGACTATATA
Found at i:16739 original size:91 final size:92
Alignment explanation
Indices: 16584--16767 Score: 334
Period size: 91 Copynumber: 2.0 Consensus size: 92
16574 AGTTAAGAAG
*
16584 TAACCATAGAAACTATGGAACCCACTATATATTTTCCCCCTACTATTTACTCCCTTGTTTTAGTT
1 TAACCATAGAAACTATGGAACCCACTATATATTTTCCCCCTACTATTTACTCCCGTGTTTTAGTT
16649 ACTATGCTTTTA-TTTTATTAATACCT
66 ACTATGCTTTTATTTTTATTAATACCT
*
16675 TAACCATAGAAACTATGGAACCCACTATATATTTTCCCCCTTCTATTTACTCCCGTGTTTTAGTT
1 TAACCATAGAAACTATGGAACCCACTATATATTTTCCCCCTACTATTTACTCCCGTGTTTTAGTT
*
16740 ACTATGCTTTTATTTTTTTTAATACCT
66 ACTATGCTTTTATTTTTATTAATACCT
16767 T
1 T
16768 TTTATGAAAA
Statistics
Matches: 89, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 75 0.84
92 14 0.16
ACGTcount: A:0.26, C:0.23, G:0.07, T:0.44
Consensus pattern (92 bp):
TAACCATAGAAACTATGGAACCCACTATATATTTTCCCCCTACTATTTACTCCCGTGTTTTAGTT
ACTATGCTTTTATTTTTATTAATACCT
Found at i:18457 original size:19 final size:20
Alignment explanation
Indices: 18430--18467 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
18420 AATTTTTGTA
18430 TATAATATAAA-ATATTTAT
1 TATAATATAAATATATTTAT
*
18449 TATATTATAAATATATTTA
1 TATAATATAAATATATTTA
18468 AAATACACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATAATATAAATATATTTAT
Found at i:21364 original size:42 final size:42
Alignment explanation
Indices: 21316--22024 Score: 503
Period size: 43 Copynumber: 16.5 Consensus size: 42
21306 ATTAGAATCA
* **
21316 TCAATTATAAAGATAAAAAGT-ATGATTGAAAAATTAGGAACC
1 TCAATTATAAAGATAAAAAGTGA-GATTAAAAAATTAGGGGCC
* * *
21358 TTAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGGCGCC
1 TCAATTATAAAGATAAAAAGTGAGATTAAAAAATTAGGGGCC
* * * **
21400 TCAATTATGAATG-TAGAGAGTGAGATTAAAAAAATTAGATGCC
1 TCAATTAT-AAAGATAAAAAGTGAGATT-AAAAAATTAGGGGCC
*
21443 TCAATTATAAAGATAAAAAGT-AGGATTGAAAAAAATAGGGGCC
1 TCAATTATAAAGATAAAAAGTGA-GATT-AAAAAATTAGGGGCC
* * * *
21486 TTAATTATAAAGGA-AAAAAGTGGGTTTACAAAAATTAGGGCCC
1 TCAATTATAAA-GATAAAAAGTGAGATTA-AAAAATTAGGGGCC
* * *
21529 TCAATTGTAAAGGA-AAAAAGTGAGATTAAAAAATTAGGGACT
1 TCAATTATAAA-GATAAAAAGTGAGATTAAAAAATTAGGGGCC
* * *
21571 TCAATTATAAATGCAT--AAAGTGAAATTTTAAAAATTAGAGGCC
1 TCAATTATAAA-G-ATAAAAAGTGAGA-TTAAAAAATTAGGGGCC
*
21614 TCAATTATAAAGGA-AAAAAGTG-GAATTGAAAAAAAAAAATCAGGGGCC
1 TCAATTATAAA-GATAAAAAGTGAG-ATT------AAAAAATTAGGGGCC
*
21662 TCAATTATAAAAGA-AAAAAGTGGGATTACAAAAATTAGGGGCC
1 TCAATTAT-AAAGATAAAAAGTGAGATTA-AAAAATTAGGGGCC
* * *
21705 TCAATTGTAAAGGA-AAAAAGTGAGATTGAAAAAAAATTAGCGGTC
1 TCAATTATAAA-GATAAAAAGTGAGATT---AAAAAATTAGGGGCC
* * * *
21750 TCAATTATAAAGGTAAAAAGTGGGATTACAAAAATTTGAGGCC
1 TCAATTATAAAGATAAAAAGTGAGATTA-AAAAATTAGGGGCC
* * * * *
21793 TCAATTACATAGGTAAAAAGTGTGATTAAAAAATTAGGGACC
1 TCAATTATAAAGATAAAAAGTGAGATTAAAAAATTAGGGGCC
* * * *
21835 TCAATTATAAATG-TAGAAAGTGAAATTAAAAAAAGTAGAGGCC
1 TCAATTATAAA-GATAAAAAGTGAGATT-AAAAAATTAGGGGCC
* * ** *
21878 TTAATTATAAAGGTAAAAAGTG-GATTGAAAAAAATTAAAGACC
1 TCAATTATAAAGATAAAAAGTGAGATT--AAAAAATTAGGGGCC
* * * * *
21921 TCAATTATAAAGGTAAAAATTGATATTATAAAAA-TAGGAGTC
1 TCAATTATAAAGATAAAAAGTGAGATTA-AAAAATTAGGGGCC
* * * * *
21963 TCAATTATAAAGATAGAAAA-TAAAATCGAAAAAATTAAGGTCC
1 TCAATTATAAAGATA-AAAAGTGAGAT-TAAAAAATTAGGGGCC
* *
22006 TTAATTATAATGATAAAAA
1 TCAATTATAAAGATAAAAA
22025 AATAATTAGG
Statistics
Matches: 539, Mismatches: 90, Indels: 76
0.76 0.13 0.11
Matches are distributed among these distances:
42 164 0.30
43 297 0.55
44 6 0.01
45 34 0.06
46 1 0.00
48 33 0.06
49 4 0.01
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (42 bp):
TCAATTATAAAGATAAAAAGTGAGATTAAAAAATTAGGGGCC
Found at i:21460 original size:85 final size:85
Alignment explanation
Indices: 21316--21982 Score: 540
Period size: 85 Copynumber: 7.7 Consensus size: 85
21306 ATTAGAATCA
* * * *
21316 TCAATTATAAA-GATAAAAAGT-ATGATT-GAAAAATTAG-GAACCTTAATTATAAAGGTAAAAA
1 TCAATTATAAATG-TAAAAAGTGA-GATTACAAAAATTAGAG-GCCTCAATTATAAAGATAAAAA
21377 GTGAGATT-AAAAAATTAGGCGCC
63 GTGAGATTAAAAAAATTAGG-GCC
* * * * *
21400 TCAATTATGAATGTAGAGAGTGAGATTAAAAAAATTAGATGCCTCAATTATAAAGATAAAAAGT-
1 TCAATTATAAATGTAAAAAGTGAGATTACAAAAATTAGAGGCCTCAATTATAAAGATAAAAAGTG
21464 AGGATTGAAAAAAA-TAGGGGCC
66 A-GATT-AAAAAAATTA-GGGCC
* * * * * *
21486 TTAATTATAAAGGAAAAAAGTGGGTTTACAAAAATTAG-GGCCCTCAATTGTAAAGGA-AAAAAG
1 TCAATTATAAATGTAAAAAGTGAGATTACAAAAATTAGAGG-CCTCAATTATAAA-GATAAAAAG
*
21549 TGAGATT-AAAAAATTAGGGACT
64 TGAGATTAAAAAAATTAGGG-CC
* * * **
21571 TCAATTATAAATGCATAAAGTGAAATTTTAAAAATTAGAGGCCTCAATTATAAAGGA-AAAAAGT
1 TCAATTATAAATGTAAAAAGTGAGATTACAAAAATTAGAGGCCTCAATTATAAA-GATAAAAAGT
*
21635 G-GAATTGAAAAAAAAAAATCAGGGGCC
65 GAG-ATT-----AAAAAAATTA-GGGCC
* * * * *
21662 TCAATTATAAAAGAAAAAAGTGGGATTACAAAAATTAGGGGCCTCAATTGTAAAGGA-AAAAAGT
1 TCAATTATAAATGTAAAAAGTGAGATTACAAAAATTAGAGGCCTCAATTATAAA-GATAAAAAGT
*
21726 GAGATTGAAAAAAAATTAGCGGTC
65 GAGATT--AAAAAAATTAG-GGCC
* * * * * *
21750 TCAATTATAAAGGTAAAAAGTGGGATTACAAAAATTTGAGGCCTCAATTACATAGGTAAAAAGTG
1 TCAATTATAAATGTAAAAAGTGAGATTACAAAAATTAGAGGCCTCAATTATAAAGATAAAAAGTG
*
21815 TGATT-AAAAAATTAGGGACC
66 AGATTAAAAAAATTAGGG-CC
* * * * * *
21835 TCAATTATAAATGTAGAAAGTGAAATTAAAAAAAGTAGAGGCCTTAATTATAAAGGTAAAAAGTG
1 TCAATTATAAATGTAAAAAGTGAGATTACAAAAATTAGAGGCCTCAATTATAAAGATAAAAAGTG
* *
21900 -GATTGAAAAAAATTAAAGACC
66 AGATT-AAAAAAATT-AGGGCC
* * * * *
21921 TCAATTATAAAGGTAAAAATTGATATTATAAAAA-TAG-GAGTCTCAATTATAAAGATAGAAAA
1 TCAATTATAAATGTAAAAAGTGAGATTACAAAAATTAGAG-GCCTCAATTATAAAGATA-AAAA
21983 TAAAATCGAA
Statistics
Matches: 478, Mismatches: 74, Indels: 60
0.78 0.12 0.10
Matches are distributed among these distances:
84 38 0.08
85 179 0.37
86 102 0.21
87 15 0.03
88 72 0.15
91 68 0.14
92 4 0.01
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (85 bp):
TCAATTATAAATGTAAAAAGTGAGATTACAAAAATTAGAGGCCTCAATTATAAAGATAAAAAGTG
AGATTAAAAAAATTAGGGCC
Found at i:21575 original size:128 final size:129
Alignment explanation
Indices: 21316--22024 Score: 581
Period size: 128 Copynumber: 5.5 Consensus size: 129
21306 ATTAGAATCA
* * **
21316 TCAATTATAAA-GATAAAAAGT-ATGATTG-AAAAATTAGGAACCTTAATTATAAAGGTAAAAAG
1 TCAATTATAAATGATAAAAAGTGA-AATTGAAAAAAATAGGGGCCTTAATTATAAAGGTAAAAAG
* * * * * * *
21378 TGAGATT-AAAAAATTA-GGCGCCTCAATTATGAATGTAGAGAGTGAGATTAAAAAAATTAGATG
65 TGGGTTTAAAAAAATTAGGGC-CCTCAATTATAAAGGTAAAAAGTGAGATT-AAAAAATTAG-GG
21441 -CC
127 ACC
* *
21443 TCAATTATAAA-GATAAAAAGT-AGGATTGAAAAAAATAGGGGCCTTAATTATAAAGGAAAAAAG
1 TCAATTATAAATGATAAAAAGTGA-AATTGAAAAAAATAGGGGCCTTAATTATAAAGGTAAAAAG
* * * *
21506 TGGGTTTACAAAAATTAGGGCCCTCAATTGTAAAGGAAAAAAGTGAGATTAAAAAATTAGGGACT
65 TGGGTTTAAAAAAATTAGGGCCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGGGACC
** * * * *
21571 TCAATTATAAATGCAT--AAAGTGAAATTTTAAAAATTAGAGGCCTCAATTATAAAGGAAAAAAG
1 TCAATTATAAATG-ATAAAAAGTGAAATTGAAAAAAATAGGGGCCTTAATTATAAAGGTAAAAAG
* * * * * * *
21634 TGGAATTGAAAAAAAAAAATCAGGGGCCTCAATTATAAAAGAAAAAAGTGGGATTACAAAAATTA
65 TGG-GTT----TAAAAAAATTAGGGCCCTCAATTATAAAGGTAAAAAGTGAGATTA-AAAAATTA
*
21699 GGGGCC
124 GGGACC
* * * * * *
21705 TCAATTGTAAAGGA-AAAAAGTGAGATTGAAAAAAAATTAGCGGTCTCAATTATAAAGGTAAAAA
1 TCAATTATAAATGATAAAAAGTGAAATTG-AAAAAAA-TAGGGGCCTTAATTATAAAGGTAAAAA
* * * * * *
21769 GTGGGATTACAAAAATTTGAGG-CCTCAATTACATAGGTAAAAAGTGTGATTAAAAAATTAGGGA
64 GTGGGTTTAAAAAAATTAG-GGCCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGGGA
21833 CC
128 CC
* *
21835 TCAATTATAAATG-TAGAAAGTGAAATT-AAAAAAAGTAGAGGCCTTAATTATAAAGGTAAAAAG
1 TCAATTATAAATGATAAAAAGTGAAATTGAAAAAAA-TAGGGGCCTTAATTATAAAGGTAAAAAG
* * ** * * *
21898 TGGATTGAAAAAAATTAAAGACCTCAATTATAAAGGTAAAAATTGATATTATAAAAA-TA-GGAG
65 TGGGTTTAAAAAAATTAGGGCCCTCAATTATAAAGGTAAAAAGTGAGATTA-AAAAATTAGGGA-
*
21961 TC
128 CC
* * * * * * *
21963 TCAATTATAAA-GATAGAAAA-TAAAATCGAAAAAATTAAGGTCCTTAATTATAATGATAAAAA
1 TCAATTATAAATGATA-AAAAGTGAAATTGAAAAAAATAGGGGCCTTAATTATAAAGGTAAAAA
22025 AATAATTAGG
Statistics
Matches: 474, Mismatches: 83, Indels: 49
0.78 0.14 0.08
Matches are distributed among these distances:
127 33 0.07
128 211 0.45
129 49 0.10
130 40 0.08
131 33 0.07
132 2 0.00
133 39 0.08
134 33 0.07
135 6 0.01
136 28 0.06
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (129 bp):
TCAATTATAAATGATAAAAAGTGAAATTGAAAAAAATAGGGGCCTTAATTATAAAGGTAAAAAGT
GGGTTTAAAAAAATTAGGGCCCTCAATTATAAAGGTAAAAAGTGAGATTAAAAAATTAGGGACC
Found at i:21822 original size:264 final size:261
Alignment explanation
Indices: 21385--21982 Score: 701
Period size: 264 Copynumber: 2.3 Consensus size: 261
21375 AAGTGAGATT
* * * * * * *
21385 AAAAAATTAGGCGCCTCAATTATGAATGTAGAGAGTGAGATTAAAAAAATTAGATGCCTCAATTA
1 AAAAAATCAGGCGCCTCAATTATAAAAGAAAAAAGTGAGATTAAAAAAATTAGAGGCCTCAATTA
* * *
21450 TAAAGATAAAAAGTAGGATTGAAAAAAATAGGGGCCTTAATTATAAAGGAAAAAAGTGGGTTTAC
66 TAAAGATAAAAAGTAGGATTGAAAAAAATAGCGGCCTCAATTATAAAGGAAAAAAGTGGGATTAC
** *
21515 AAAAATTAGGGCCCTCAATTGTAAAGGAAAAAAGTGAGATTAAAAAATTAGGGACTTCAATTATA
131 AAAAATTAGGGCCCTCAATTACAAAGGAAAAAAGTGAGATTAAAAAATTAGGGACCTCAATTATA
* ** *
21580 AATGCATAAAGTGAAATTTTAAAAATTAGAGGCCTCAATTATAAAGGAAAAAAGTGGAATTGAAA
196 AATGCAGAAAGTGAAATTAAAAAAAGTAGAGGCCTCAATTATAAAGGAAAAAAGTGG-ATTGAAA
21645 AA
260 AA
* * * * *
21647 AAAAAATCAGGGGCCTCAATTATAAAAGAAAAAAGTGGGATTACAAAAATTAGGGGCCTCAATTG
1 AAAAAATCAGGCGCCTCAATTATAAAAGAAAAAAGTGAGATTAAAAAAATTAGAGGCCTCAATTA
* *
21712 TAAAGGA-AAAAAGT-GAGATTGAAAAAAAATTAGCGGTCTCAATTATAAAGGTAAAAAGTGGGA
66 TAAA-GATAAAAAGTAG-GATTG-AAAAAAA-TAGCGGCCTCAATTATAAAGGAAAAAAGTGGGA
* * * *
21775 TTACAAAAATTTGAGG-CCTCAATTACATAGGTAAAAAGTGTGATTAAAAAATTAGGGACCTCAA
127 TTACAAAAATTAG-GGCCCTCAATTACAAAGGAAAAAAGTGAGATTAAAAAATTAGGGACCTCAA
* * *
21839 TTATAAATGTAGAAAGTGAAATTAAAAAAAGTAGAGGCCTTAATTATAAAGGTAAAAAGTGGATT
191 TTATAAATGCAGAAAGTGAAATTAAAAAAAGTAGAGGCCTCAATTATAAAGGAAAAAAGTGGATT
21904 GAAAAA
256 GAAAAA
** * * * * * * *
21910 AATTAA--A-G-ACCTCAATTATAAAGGTAAAAATTGATATTATAAAAA-TAG-GAGTCTCAATT
1 AAAAAATCAGGCGCCTCAATTATAAAAGAAAAAAGTGAGATTAAAAAAATTAGAG-GCCTCAATT
21969 ATAAAGATAGAAAA
65 ATAAAGATA-AAAA
21983 TAAAATCGAA
Statistics
Matches: 286, Mismatches: 42, Indels: 19
0.82 0.12 0.05
Matches are distributed among these distances:
257 3 0.01
258 16 0.06
259 34 0.12
260 1 0.00
261 2 0.01
262 69 0.24
263 22 0.08
264 137 0.48
265 2 0.01
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (261 bp):
AAAAAATCAGGCGCCTCAATTATAAAAGAAAAAAGTGAGATTAAAAAAATTAGAGGCCTCAATTA
TAAAGATAAAAAGTAGGATTGAAAAAAATAGCGGCCTCAATTATAAAGGAAAAAAGTGGGATTAC
AAAAATTAGGGCCCTCAATTACAAAGGAAAAAAGTGAGATTAAAAAATTAGGGACCTCAATTATA
AATGCAGAAAGTGAAATTAAAAAAAGTAGAGGCCTCAATTATAAAGGAAAAAAGTGGATTGAAAA
A
Found at i:22881 original size:22 final size:22
Alignment explanation
Indices: 22854--22896 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
22844 ATTATTATTT
22854 TTTAACAAATTCAGTAAAAAAA
1 TTTAACAAATTCAGTAAAAAAA
22876 TTTAACAAATTCAGTAAAAAA
1 TTTAACAAATTCAGTAAAAAA
22897 TTACCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.28
Consensus pattern (22 bp):
TTTAACAAATTCAGTAAAAAAA
Found at i:22923 original size:21 final size:21
Alignment explanation
Indices: 22897--22940 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
22887 CAGTAAAAAA
*
22897 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATTAATATTT
*
22918 TTACCTAAAATATTAATATTT
1 TTACCTAAAACATTAATATTT
22939 TT
1 TT
22941 TAACATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (21 bp):
TTACCTAAAACATTAATATTT
Found at i:23363 original size:12 final size:13
Alignment explanation
Indices: 23327--23370 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
23317 GCCCCGATTA
*
23327 CCCGATTACCAGC
1 CCCGATTACCCGC
23340 CCCGATTACCCGC
1 CCCGATTACCCGC
*
23353 CCCGA-TACCCGA
1 CCCGATTACCCGC
23365 CCCGAT
1 CCCGAT
23371 AAATATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.20, C:0.50, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:23510 original size:12 final size:12
Alignment explanation
Indices: 23495--23529 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
23485 CGATTCTCGG
23495 CCCAATACCCGA
1 CCCAATACCCGA
*
23507 CCCAATACCCGG
1 CCCAATACCCGA
23519 CCCAATACCCG
1 CCCAATACCCG
23530 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:28615 original size:14 final size:14
Alignment explanation
Indices: 28596--28634 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
28586 TAATGGGGAG
28596 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
28610 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
28624 GAATCTCTGCA
1 TAATCCCTGCA
28635 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:31991 original size:16 final size:16
Alignment explanation
Indices: 31970--32000 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31960 ATCATCATAT
*
31970 ATATTTTTATGTTAGA
1 ATATTTTTATATTAGA
31986 ATATTTTTATATTAG
1 ATATTTTTATATTAG
32001 TTTTGGTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (16 bp):
ATATTTTTATATTAGA
Found at i:43847 original size:6 final size:6
Alignment explanation
Indices: 43826--43862 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
43816 TCTCGTCTCG
43826 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
43863 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:43990 original size:21 final size:20
Alignment explanation
Indices: 43966--44094 Score: 109
Period size: 21 Copynumber: 6.2 Consensus size: 20
43956 ACTATCGTAA
43966 TGCGATAGTCCAAGTTCGCAT
1 TGCGATAGTCCAA-TTCGCAT
* *
43987 TGCGATAGTCGACTATCGCAT
1 TGCGATAGTCCAAT-TCGCAT
* *
44008 TGCGAT-TTACATATTCGCAT
1 TGCGATAGTCCA-ATTCGCAT
* *
44028 TACGATAGTCCAAGTTTGCAT
1 TGCGATAGTCCAA-TTCGCAT
* *
44049 TGCGAT-TTACATATTCGCAT
1 TGCGATAGTCCA-ATTCGCAT
*
44069 TGCGATAGTCCAAAATCGCAT
1 TGCGATAGTCC-AATTCGCAT
44090 TGCGA
1 TGCGA
44095 GTCTGGAAAC
Statistics
Matches: 84, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
20 30 0.36
21 53 0.63
22 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (20 bp):
TGCGATAGTCCAATTCGCAT
Found at i:44027 original size:20 final size:20
Alignment explanation
Indices: 44002--44074 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
43992 TAGTCGACTA
44002 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* * *
44022 TCGCATTACGATAGTCCA-AGT
1 TCGCATTGCGAT-TTACATA-T
*
44043 TTGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
44063 TCGCATTGCGAT
1 TCGCATTGCGAT
44075 AGTCCAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:44035 original size:41 final size:41
Alignment explanation
Indices: 43980--44094 Score: 153
Period size: 41 Copynumber: 2.8 Consensus size: 41
43970 ATAGTCCAAG
* *
43980 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCAAATATCGCATTGCGATTTACATA
* * *
44021 TTCGCATTACGATAGTCCAAGT-TTGCATTGCGATTTACATA
1 TTCGCATTGCGATAGT-CAAATATCGCATTGCGATTTACATA
44062 TTCGCATTGCGATAGTCCAAA-ATCGCATTGCGA
1 TTCGCATTGCGATAGT-CAAATATCGCATTGCGA
44095 GTCTGGAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
41 62 0.95
42 3 0.05
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCAAATATCGCATTGCGATTTACATA
Found at i:44088 original size:62 final size:62
Alignment explanation
Indices: 43968--44090 Score: 144
Period size: 62 Copynumber: 2.0 Consensus size: 62
43958 TATCGTAATG
* * *
43968 CGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCGCATTA
1 CGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATGTACAAAATCGCATTA
* * *
44030 CGATAGTCCAAGTTTGCATTGCGAT--T-TACATATTCGCATTGCGATAGTCCAAAATCGCATT
1 CGATAGTCCAAGTTCGCATTGCGATAGTCGAC-TA-TCGCATTGCGAT-GTACAAAATCGCATT
44091 GCGAGTCTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
59 2 0.04
60 3 0.06
61 12 0.23
62 35 0.67
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (62 bp):
CGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATGTACAAAATCGCATTA
Found at i:44519 original size:2 final size:2
Alignment explanation
Indices: 44512--44550 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
44502 ATATCAATGT
44512 TA TA TA 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 TA TA TA T
44551 TATGGGTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44857 original size:28 final size:28
Alignment explanation
Indices: 44824--44879 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
44814 ATCGTCATTG
* *
44824 CTTTCAAGTATTGAATCGACGGTATAAT
1 CTTTCAAGTACTGAATCGACAGTATAAT
**
44852 CTTTCAAGTACTGGCTCGACAGTATAAT
1 CTTTCAAGTACTGAATCGACAGTATAAT
44880 GTAAACAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (28 bp):
CTTTCAAGTACTGAATCGACAGTATAAT
Found at i:45352 original size:13 final size:13
Alignment explanation
Indices: 45334--45361 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
45324 TTTGTTTTAA
45334 GATAGCACGTGAT
1 GATAGCACGTGAT
45347 GATAGCACGTGAT
1 GATAGCACGTGAT
45360 GA
1 GA
45362 GCGATAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.14, G:0.32, T:0.21
Consensus pattern (13 bp):
GATAGCACGTGAT
Found at i:45472 original size:2 final size:2
Alignment explanation
Indices: 45467--45494 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45457 TTAATTAACA
45467 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
45495 TACGAACGAA
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:48152 original size:16 final size:16
Alignment explanation
Indices: 48128--48164 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
48118 GAAAATTTAA
48128 AATTATTATATATTTT
1 AATTATTATATATTTT
*
48144 AATTTTTATATATTTT
1 AATTATTATATATTTT
*
48160 TATTA
1 AATTA
48165 AAAATATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
AATTATTATATATTTT
Found at i:52799 original size:15 final size:15
Alignment explanation
Indices: 52775--52810 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
52765 ATACCATTAA
*
52775 ATTAATTTATAAAAC
1 ATTAAATTATAAAAC
*
52790 ATTAAATTATAAAAT
1 ATTAAATTATAAAAC
52805 ATTAAA
1 ATTAAA
52811 CATTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:52860 original size:16 final size:16
Alignment explanation
Indices: 52839--52876 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
52829 TTAAAAATCT
52839 AAATATAAT-TTAATTA
1 AAATATAATATTAA-TA
*
52855 AAATATAATATTTATA
1 AAATATAATATTAATA
52871 AAATAT
1 AAATAT
52877 TAGTTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATAATATTAATA
Found at i:59140 original size:180 final size:180
Alignment explanation
Indices: 58838--59173 Score: 663
Period size: 180 Copynumber: 1.9 Consensus size: 180
58828 ATATTTTTAT
58838 AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
1 AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
58903 CAAAAATAATTTTTCTAAAATGAAATAAAACTATGTAGTACTTTAAATAAATTGATACATTACAC
66 CAAAAATAATTTTTCTAAAATGAAATAAAACTATGTAGTACTTTAAATAAATTGATACATTACAC
58968 AAACACCATATAAGAATGATAATTACCCCAAAACAATAAATACTTACTCC
131 AAACACCATATAAGAATGATAATTACCCCAAAACAATAAATACTTACTCC
59018 AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
1 AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
59083 CAAAAATAATTTTTCTAAAATGAAATAAAACTATGTAGTACTTTAAATAAATTGATACATTACAC
66 CAAAAATAATTTTTCTAAAATGAAATAAAACTATGTAGTACTTTAAATAAATTGATACATTACAC
*
59148 AAATACCATATAAGAATGATAATTAC
131 AAACACCATATAAGAATGATAATTAC
59174 ATAGAATATA
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
180 155 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (180 bp):
AAATATAATTACTATAAAAATATTTAAATATATAAAATCAAATCACTATATACCACCAACGTGGA
CAAAAATAATTTTTCTAAAATGAAATAAAACTATGTAGTACTTTAAATAAATTGATACATTACAC
AAACACCATATAAGAATGATAATTACCCCAAAACAATAAATACTTACTCC
Found at i:61850 original size:2 final size:2
Alignment explanation
Indices: 61843--61867 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61833 GCATGGTGTA
61843 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
61868 CCAGTAATTG
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:69500 original size:13 final size:13
Alignment explanation
Indices: 69479--69538 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
69469 ATTTTGTTAG
69479 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
69492 TATTGTA-TTATT
1 TATTTTATTTAAT
69504 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
69516 TATTTTATTTAAT
1 TATTTTATTTAAT
69529 TATTTTATTT
1 TATTTTATTT
69539 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:69504 original size:21 final size:20
Alignment explanation
Indices: 69479--69543 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
69469 ATTTTGTTAG
69479 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
69500 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
69516 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
*
69537 TTTTTTA
1 TATTTTA
69544 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 2 0.06
19 2 0.06
20 6 0.17
21 13 0.36
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:69514 original size:29 final size:29
Alignment explanation
Indices: 69481--69543 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
69471 TTTGTTAGTA
69481 TTTTATT-TAATTATTGT-ATTATTTAATTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTT
* *
69510 TTTTATTATTTTATTTAATTATTTTATTT
1 TTTTATTATATTATTTAATTATTTAATTT
69539 TTTTA
1 TTTTA
69544 CAGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATTATTTAATTATTTAATTT
Found at i:69525 original size:16 final size:16
Alignment explanation
Indices: 69483--69525 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
69473 TGTTAGTATT
* *
69483 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
69499 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
69515 TTATTTTATTT
1 TTATTTAATTT
69526 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:69811 original size:8 final size:8
Alignment explanation
Indices: 69800--69871 Score: 50
Period size: 8 Copynumber: 9.8 Consensus size: 8
69790 TAAAAAAATA
69800 AAATAATT
1 AAATAATT
69808 AAAT-A--
1 AAATAATT
*
69813 AAATAATA
1 AAATAATT
*
69821 AAAAAATT
1 AAATAATT
69829 AAATAA--
1 AAATAATT
*
69835 AAA-AATA
1 AAATAATT
*
69842 AAAAAATT
1 AAATAATT
69850 AAATAA-T
1 AAATAATT
69857 ACAATAATT
1 A-AATAATT
69866 AAATAA
1 AAATAA
69872 AATACTAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
5 6 0.12
6 4 0.08
7 6 0.12
8 33 0.65
9 2 0.04
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (8 bp):
AAATAATT
Found at i:69813 original size:13 final size:13
Alignment explanation
Indices: 69795--69875 Score: 70
Period size: 13 Copynumber: 6.8 Consensus size: 13
69785 AACTGTAAAA
69795 AAATAAAATAATT
1 AAATAAAATAATT
69808 AAATAAAATAA-T
1 AAATAAAATAATT
69820 --A-AAAA-AATT
1 AAATAAAATAATT
*
69829 AAATAAAA-AAAT
1 AAATAAAATAATT
*
69841 AAA-AAAATTAAAT
1 AAATAAAA-TAATT
*
69854 -AATACAATAATT
1 AAATAAAATAATT
69866 AAATAAAATA
1 AAATAAAATA
69876 CTAACAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
8 2 0.04
9 5 0.09
10 1 0.02
11 5 0.09
12 17 0.30
13 26 0.46
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (13 bp):
AAATAAAATAATT
Found at i:69827 original size:29 final size:29
Alignment explanation
Indices: 69790--69886 Score: 113
Period size: 29 Copynumber: 3.3 Consensus size: 29
69780 TTTATAACTG
69790 TAAAAAAATAAAATAATTAAATAAAATAA
1 TAAAAAAATAAAATAATTAAATAAAATAA
* ** *
69819 TAAAAAAATTAAATAAAAAAATAAAAAAA
1 TAAAAAAATAAAATAATTAAATAAAATAA
* * * *
69848 TTAAATAATACAATAATTAAATAAAATAC
1 TAAAAAAATAAAATAATTAAATAAAATAA
*
69877 TAACAAAATA
1 TAAAAAAATA
69887 TGATTAATTT
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (29 bp):
TAAAAAAATAAAATAATTAAATAAAATAA
Found at i:69863 original size:21 final size:21
Alignment explanation
Indices: 69790--69855 Score: 114
Period size: 21 Copynumber: 3.1 Consensus size: 21
69780 TTTATAACTG
*
69790 TAAAAAAATAAAATAATTAAA
1 TAAAAAAATAAAAAAATTAAA
*
69811 TAAAATAATAAAAAAATTAAA
1 TAAAAAAATAAAAAAATTAAA
69832 TAAAAAAATAAAAAAATTAAA
1 TAAAAAAATAAAAAAATTAAA
69853 TAA
1 TAA
69856 TACAATAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (21 bp):
TAAAAAAATAAAAAAATTAAA
Found at i:78609 original size:5 final size:5
Alignment explanation
Indices: 78599--78626 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
78589 AGCGAAAGAA
78599 GAATG GAATG GAATG GAATG GAATG GAA
1 GAATG GAATG GAATG GAATG GAATG GAA
78627 ACCGAGAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.18
Consensus pattern (5 bp):
GAATG
Found at i:86186 original size:11 final size:10
Alignment explanation
Indices: 86170--86205 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
86160 TTTGCCTCTT
86170 TTCTTTGAGG
1 TTCTTTGAGG
86180 ATTCTTTGAGG
1 -TTCTTTGAGG
*
86191 TTCTTGGAGG
1 TTCTTTGAGG
86201 TTCTT
1 TTCTT
86206 GAAGATGGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.11, C:0.11, G:0.28, T:0.50
Consensus pattern (10 bp):
TTCTTTGAGG
Found at i:87368 original size:265 final size:262
Alignment explanation
Indices: 86868--87394 Score: 1000
Period size: 265 Copynumber: 2.0 Consensus size: 262
86858 CTCTGATACC
86868 ATGTAAAGATTATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
1 ATGTAAAGATTATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
*
86933 ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAATATTCTCAAGGAGAGTATTTATAGCTAGT
66 ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAAAATTCTCAAGGAGAGTATTTATAGCTAGT
86998 ACTAGCTGAAACTGATGTAACTAATTTCACAACAAACTAACTGCTTCAACTGATCAGCTGCAGTG
131 ACTAGCTGAAACTGATGTAACTAATTTCACAACAAACTAACTGCTTCAACTGATCAGCTGCAGTG
87063 AACCAATCCTTAACTGCACAACCATCATGCACAGCAGTTGCACGTGTTGCATTCACATACACTAA
196 AACCAATCCTTAACTGCACAACCATCATGCACAGCAGTTGCACGTGTTGCATTCACATACACTAA
87128 CA
261 CA
87130 ATGTAAAGATTATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
1 ATGTAAAGATTATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
87195 ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAACAATTCTCAAGGAGAGTATTTATAGCTAG
66 ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAA-AATTCTCAAGGAGAGTATTTATAGCTAG
87260 TACTATAGCTGAAACTGATGTAACTAATTTCACAACAAACTAACTGCTTCAACTGATCAGCTGCA
130 TAC--TAGCTGAAACTGATGTAACTAATTTCACAACAAACTAACTGCTTCAACTGATCAGCTGCA
* *
87325 GTGAACCAATCCTTAGCTGCACAACCATCATGCACATCAGTTGCACGTGTTGCATTCACATACAC
193 GTGAACCAATCCTTAACTGCACAACCATCATGCACAGCAGTTGCACGTGTTGCATTCACATACAC
87390 TAACA
258 TAACA
87395 TTCCCCTTGT
Statistics
Matches: 259, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
262 101 0.39
263 30 0.12
265 128 0.49
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (262 bp):
ATGTAAAGATTATGAACAAATGTCTAAGCTATGAAAGTAAGAACAAAGAGAATAAACGAAAGAGA
ACTTCTGAAATTCATTATCTTTAAGAGTGTTTATAAAATTCTCAAGGAGAGTATTTATAGCTAGT
ACTAGCTGAAACTGATGTAACTAATTTCACAACAAACTAACTGCTTCAACTGATCAGCTGCAGTG
AACCAATCCTTAACTGCACAACCATCATGCACAGCAGTTGCACGTGTTGCATTCACATACACTAA
CA
Found at i:89732 original size:8 final size:7
Alignment explanation
Indices: 89703--89737 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
89693 AAATTATGGA
89703 TTAAATT
1 TTAAATT
89710 TTAAATT
1 TTAAATT
89717 TTAAATT
1 TTAAATT
*
89724 TTAAAAT
1 TTAAATT
89731 TTAAATT
1 TTAAATT
89738 AAAATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTAAATT
Done.