Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008524.1 Hibiscus syriacus cultivar Beakdansim tig00111393_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: 760704
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:590667 original size:47 final size:47
Alignment explanation
Indices: 590576--590669 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 47
590566 TTACATGATA
* * * *
590576 AAAAATAATATTATTCTTTTTAAAGATTTTAAGTTTGAGTAATTATT
1 AAAAATAATATCATTCTTTCTAAAGATTTTAAGTTTAAGCAATTATT
* *
590623 AAAAATAATGTCATT-TTTCTAAAGATTTTAGGTTTTAAGCAATTATT
1 AAAAATAATATCATTCTTTCTAAAGATTTTAAG-TTTAAGCAATTATT
590670 CTTTCTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
46 15 0.38
47 25 0.62
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (47 bp):
AAAAATAATATCATTCTTTCTAAAGATTTTAAGTTTAAGCAATTATT
Found at i:593834 original size:44 final size:44
Alignment explanation
Indices: 593778--593867 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
593768 TGTAATTGGG
593778 CTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGGGATTTGGGGA
1 CTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGGGATTTGGGGA
593822 CTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGGGATTTGGGGA
1 CTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGGGATTTGGGGA
593866 CT
1 CT
593868 AGGGTTTTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (44 bp):
CTTTTTTTATTTGTTATTTGTTTCAGTAGCTAGGGATTTGGGGA
Found at i:614080 original size:21 final size:21
Alignment explanation
Indices: 614054--614099 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
614044 CTTTGCTGTT
614054 GGAGGAAGCTATGGCTACATG
1 GGAGGAAGCTATGGCTACATG
614075 GGAGGAAGCTATGGCTACATG
1 GGAGGAAGCTATGGCTACATG
614096 GGAG
1 GGAG
614100 ATTAGCAGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.41, T:0.17
Consensus pattern (21 bp):
GGAGGAAGCTATGGCTACATG
Found at i:619172 original size:27 final size:27
Alignment explanation
Indices: 619141--619235 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
619131 TCTATTTACA
*
619141 AAATCATATCTCTACAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
619168 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
*
619195 AAATCATATCTCTATAGGAATGATAAC
1 AAATCATATCTCTATAGGAATGGTAAC
619222 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
619236 ATTCCTACAC
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 9 0.14
27 57 0.86
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:622964 original size:27 final size:27
Alignment explanation
Indices: 622933--623000 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
622923 TCTATTTACA
622933 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
622960 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
622987 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
623001 ATTCCTACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:623331 original size:49 final size:49
Alignment explanation
Indices: 623259--623363 Score: 201
Period size: 49 Copynumber: 2.1 Consensus size: 49
623249 GGTTAACATG
623259 TTAGTAATCTCAACCTTTTCTGAGATGGGTGTTTTAGCGTAATACTAGA
1 TTAGTAATCTCAACCTTTTCTGAGATGGGTGTTTTAGCGTAATACTAGA
623308 TTAGTAATCTCAACCTTTTCTGAGATGGGTGTTTTAGCGTAATACTAGA
1 TTAGTAATCTCAACCTTTTCTGAGATGGGTGTTTTAGCGTAATACTAGA
623357 TCTAGTA
1 T-TAGTA
623364 CCTCCTTTTC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 50 0.91
50 5 0.09
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (49 bp):
TTAGTAATCTCAACCTTTTCTGAGATGGGTGTTTTAGCGTAATACTAGA
Found at i:630734 original size:15 final size:15
Alignment explanation
Indices: 630690--630735 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
630680 TTTCTTCTGG
*
630690 TTTTGATCACTTA-A
1 TTTTAATCACTTATA
*
630704 CTTTTAATTA-TTATA
1 -TTTTAATCACTTATA
630719 TTTTAATCACTTATA
1 TTTTAATCACTTATA
630734 TT
1 TT
630736 ATCAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (15 bp):
TTTTAATCACTTATA
Found at i:634040 original size:45 final size:45
Alignment explanation
Indices: 633976--634067 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
633966 GTGGCAAAGA
*
633976 TCAGGTTGCCTATAGGTCTACGAGAGAGGAGATGACTATGAGGAT
1 TCAGGTTGCCTAGAGGTCTACGAGAGAGGAGATGACTATGAGGAT
634021 TCAGGTTGCCTAGAGGTCTACGAGAGAGGAGATGACTATGAGGAT
1 TCAGGTTGCCTAGAGGTCTACGAGAGAGGAGATGACTATGAGGAT
634066 TC
1 TC
634068 TGACTTTCTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.24
Consensus pattern (45 bp):
TCAGGTTGCCTAGAGGTCTACGAGAGAGGAGATGACTATGAGGAT
Found at i:640473 original size:20 final size:20
Alignment explanation
Indices: 640445--640512 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
640435 ATTTCTAGGT
*
640445 TGTACTATTGATATTGATCA
1 TGTAATATTGATATTGATCA
* * *
640465 TGTAGTATTAATACT-ATTCA
1 TGTAATATTGATATTGA-TCA
*
640485 TGTAATATTGATATTGTTCA
1 TGTAATATTGATATTGATCA
640505 TGTAATAT
1 TGTAATAT
640513 CAATAAGTGT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.47
Consensus pattern (20 bp):
TGTAATATTGATATTGATCA
Found at i:645652 original size:16 final size:16
Alignment explanation
Indices: 645633--645666 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
645623 CAATATACGA
645633 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
645649 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
645665 AT
1 AT
645667 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:646415 original size:128 final size:126
Alignment explanation
Indices: 646206--646463 Score: 408
Period size: 128 Copynumber: 2.0 Consensus size: 126
646196 AATTTTCTTC
* *
646206 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
646271 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT--CATATAAA
* * * *
646334 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTTAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
646399 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATTATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATCATATAAA
646460 TAAT
1 TAAT
646464 AAAGACTGAA
Statistics
Matches: 120, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
126 11 0.09
128 109 0.91
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (126 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATCATATAAA
Found at i:646898 original size:35 final size:35
Alignment explanation
Indices: 646848--646923 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
646838 AATTGAATTT
* *
646848 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
646883 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
646918 AATTGA
1 AATTGA
646924 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:652201 original size:23 final size:23
Alignment explanation
Indices: 652175--652220 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
652165 TCCTCAATGT
* *
652175 TTATATTTTTATTAATTTAATTA
1 TTATATTTTCATTAAGTTAATTA
* *
652198 TTATCTTTTCCTTAAGTTAATTA
1 TTATATTTTCATTAAGTTAATTA
652221 ACCTCTATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (23 bp):
TTATATTTTCATTAAGTTAATTA
Found at i:655665 original size:179 final size:180
Alignment explanation
Indices: 655329--655667 Score: 441
Period size: 179 Copynumber: 1.9 Consensus size: 180
655319 AAACATAAGA
* * *
655329 AACTGACTTGTACACTAATGCAATAATGAGAGAGTTTAACATAATTAGCAAGCACATTCCAGTTG
1 AACTGACTTGTACACTAATGCAATAATGAGAGAGTTTAACAGAACTAGCAAGCACATTCCAGTCG
* * *
655394 AGAAATCCTCAACCGGACACACTCGTAAAGCGAGAAACATAAGTCAATCTTATTCAAAAGCCTAG
66 AGAAATCCTCAACCGGACACACTCATAAAGCGAGAAACATAAGTCAATCTTATCCAAAAGCCTAA
* ** * *
655459 TAGTTGGCAATTTCAACGACTACATATGCATGTTATGACTCCCCAGAAGC
131 AAGTCAGCAACTTCAACGACAACATATGCATGTTATGACTCCCCAGAAGC
*
655509 AACTGACTTGTACACTAATGCAATGATGAGAGAG-TTAACAGAACTAGCAAGCACATTCCAGTCG
1 AACTGACTTGTACACTAATGCAATAATGAGAGAGTTTAACAGAACTAGCAAGCACATTCCAGTCG
* * * * * * * *
655573 AGAATTCCTCAGCTGGACATA-TCCATAAATCGAGAAATATAGGTCCAA-CTTCTCCAAAAGCCT
66 AGAAATCCTCAACCGGACACACT-CATAAAGCGAGAAACATAAGT-CAATCTTATCCAAAAGCCT
**
655636 AAAAGTCAGCAACTTCAATTACAACATATGCA
129 AAAAGTCAGCAACTTCAACGACAACATATGCA
655668 ATGACTCCCC
Statistics
Matches: 135, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
178 1 0.01
179 98 0.73
180 36 0.27
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (180 bp):
AACTGACTTGTACACTAATGCAATAATGAGAGAGTTTAACAGAACTAGCAAGCACATTCCAGTCG
AGAAATCCTCAACCGGACACACTCATAAAGCGAGAAACATAAGTCAATCTTATCCAAAAGCCTAA
AAGTCAGCAACTTCAACGACAACATATGCATGTTATGACTCCCCAGAAGC
Found at i:666445 original size:159 final size:158
Alignment explanation
Indices: 666211--666818 Score: 618
Period size: 159 Copynumber: 3.8 Consensus size: 158
666201 CCTTCGTAAT
* * * *
666211 ATGCTTTCTTCAGAGATCCTA-AAAAAACT-CAGCGTTGAGAGATTTGGATTTAGTGGAAGATGT
1 ATGCTTTCTTCAGAGA-CCTATGAAAAA-TGCAGCATTGAGAGATCTGGATTTAGTGGAAGAAGT
*
666274 GATGAAAGAGATTCAGGGAACAGTTACGGGGAAAGAAGAAATATTGAAGATGGTAAAGAATCTCA
64 GATGAAAGAGATTCAGGAAACAGTTACGGGGAAAGAAGAAATATTGAA-ATGGTAAAGAATCTCA
* * * **
666339 AAATCATGGTGATCGCAGTCACCTTCATATT
128 AAAACACGGTGATCGCAGTGACCTTCATAGA
* *** * *
666370 ATGCTTTCTTCAGAGATCT-TCGAAAAATGCAGTGCTGAGAGATCTGGATTTAGTAGAGGAAGTG
1 ATGCTTTCTTCAGAGACCTAT-GAAAAATGCAGCATTGAGAGATCTGGATTTAGTGGAAGAAGTG
* ** * *
666434 CTGAAAGAGATTCAGGAAACAGTTGTGGGGAAAGAAGAAATAATAGAAATTGTAAAGAATCTCAA
65 ATGAAAGAGATTCAGGAAACAGTTACGGGGAAAGAAGAAAT-ATTGAAATGGTAAAGAATCTCAA
* * *
666499 AAACACGTTCATTGCAGTGACCTTCATAGA
129 AAACACGGTGATCGCAGTGACCTTCATAGA
* * * *
666529 ATGCTCTT-TTCGGATACCTATGAACAAA-GCAGCATTGAGAGATCTGGATTTAGTGGAAGTAGC
1 ATGCT-TTCTTCAGAGACCTATGAA-AAATGCAGCATTGAGAGATCTGGATTTAGTGGAAGAAGT
* * * * * *
666592 GAT-AAATCAGATTCAGGAGACAGTTACTGTGAAAGAAGAAATAATGGAGATGGTAAAGAATCTC
64 GATGAAA-GAGATTCAGGAAACAGTTACGGGGAAAGAAGAAAT-ATTGAAATGGTAAAGAATCTC
* * *
666656 AAAAAAACAGTGATCGCAGTGATCTTCATAGA
127 AAAAACACGGTGATCGCAGTGACCTTCATAGA
* * ** * *
666688 ATGCTTTATTCAG-GTACCTATGAACAACACAGCATTGAGAGATCTGGATTCAGTGGAAGAAATG
1 ATGCTTTCTTCAGAG-ACCTATGAAAAATGCAGCATTGAGAGATCTGGATTTAGTGGAAGAAGTG
* * * * ** *
666752 ATGATAGTGAATCAGGAAACAGTTATGATGAAAGAAGAAATCTTGGAAATGGTAAAGAATCTCAA
65 ATGAAAGAGATTCAGGAAACAGTTACGGGGAAAGAAGAAATATT-GAAATGGTAAAGAATCTCAA
666817 AA
129 AA
666819 GCATGATGAT
Statistics
Matches: 369, Mismatches: 67, Indels: 26
0.80 0.15 0.06
Matches are distributed among these distances:
158 11 0.03
159 345 0.93
160 13 0.04
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.25
Consensus pattern (158 bp):
ATGCTTTCTTCAGAGACCTATGAAAAATGCAGCATTGAGAGATCTGGATTTAGTGGAAGAAGTGA
TGAAAGAGATTCAGGAAACAGTTACGGGGAAAGAAGAAATATTGAAATGGTAAAGAATCTCAAAA
ACACGGTGATCGCAGTGACCTTCATAGA
Found at i:672455 original size:13 final size:13
Alignment explanation
Indices: 672439--672469 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
672429 CAACGGGTCA
672439 GGTCGGGTAAACG
1 GGTCGGGTAAACG
672452 GGTCGGGTAAACG
1 GGTCGGGTAAACG
672465 GGTCG
1 GGTCG
672470 TGACCGGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.48, T:0.16
Consensus pattern (13 bp):
GGTCGGGTAAACG
Found at i:679650 original size:13 final size:13
Alignment explanation
Indices: 679634--679664 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
679624 GTCAACGGGT
*
679634 CGGGTCGGGTAAA
1 CGGGTCAGGTAAA
679647 CGGGTCAGGTAAA
1 CGGGTCAGGTAAA
679660 CGGGT
1 CGGGT
679665 AAACGAGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.16, G:0.45, T:0.16
Consensus pattern (13 bp):
CGGGTCAGGTAAA
Found at i:679716 original size:19 final size:20
Alignment explanation
Indices: 679677--679722 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
679667 ACGAGTCGTG
*
679677 ACCGGTCAAACCGGTTCAAA
1 ACCGGTTAAACCGGTTCAAA
*
679697 ACTGGTTAAACCGG-TCAAA
1 ACCGGTTAAACCGGTTCAAA
679716 ACCGGTT
1 ACCGGTT
679723 TCCAGCGTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.20
Consensus pattern (20 bp):
ACCGGTTAAACCGGTTCAAA
Found at i:691849 original size:24 final size:23
Alignment explanation
Indices: 691818--691863 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
691808 AAATTAAATA
691818 TATTTT-AATTGATGTTATAATTG
1 TATTTTAAATT-ATGTTATAATTG
*
691841 TATTCTTAAATTATTTTATAATT
1 TATT-TTAAATTATGTTATAATT
691864 TAAGTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (23 bp):
TATTTTAAATTATGTTATAATTG
Found at i:698553 original size:20 final size:22
Alignment explanation
Indices: 698525--698568 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
698515 AAATTTTATG
698525 TTAAAGAGA-GA-TTTATAAAA
1 TTAAAGAGATGAGTTTATAAAA
*
698545 TTAAGGAGATGAGTTTATAAAA
1 TTAAAGAGATGAGTTTATAAAA
698567 TT
1 TT
698569 TGATGAGACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 2 0.10
22 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (22 bp):
TTAAAGAGATGAGTTTATAAAA
Found at i:703899 original size:108 final size:108
Alignment explanation
Indices: 703710--703925 Score: 423
Period size: 108 Copynumber: 2.0 Consensus size: 108
703700 TATTTTATAC
*
703710 ATTCTCGAAATGTCAGGTGACGCTTAAATATTAAAAGATATTTCATACAATTGAAGAGTCTAATA
1 ATTCTCGAAATGTCAGGTGACGCTTAAATATTAAAAGAGATTTCATACAATTGAAGAGTCTAATA
703775 GAGATCTTATATTTGATAGGATGACTTAAGTAGATTAACATGT
66 GAGATCTTATATTTGATAGGATGACTTAAGTAGATTAACATGT
703818 ATTCTCGAAATGTCAGGTGACGCTTAAATATTAAAAGAGATTTCATACAATTGAAGAGTCTAATA
1 ATTCTCGAAATGTCAGGTGACGCTTAAATATTAAAAGAGATTTCATACAATTGAAGAGTCTAATA
703883 GAGATCTTATATTTGATAGGATGACTTAAGTAGATTAACATGT
66 GAGATCTTATATTTGATAGGATGACTTAAGTAGATTAACATGT
703926 TCGATAGAGT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (108 bp):
ATTCTCGAAATGTCAGGTGACGCTTAAATATTAAAAGAGATTTCATACAATTGAAGAGTCTAATA
GAGATCTTATATTTGATAGGATGACTTAAGTAGATTAACATGT
Found at i:707137 original size:30 final size:30
Alignment explanation
Indices: 707072--707129 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
707062 CTTTTTTAGA
*
707072 ACTTAGATGAAAAAAATTGAATACTTTAAAT
1 ACTTAGATGAAAAAAAAT-AATACTTTAAAT
707103 ACTTAGATGAAAAAATAAT-ATACTTTA
1 ACTTAGATGAAAAAA-AATAATACTTTA
707130 GGTACTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 15 0.60
32 2 0.08
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.33
Consensus pattern (30 bp):
ACTTAGATGAAAAAAAATAATACTTTAAAT
Found at i:713894 original size:49 final size:50
Alignment explanation
Indices: 713791--713895 Score: 119
Period size: 49 Copynumber: 2.1 Consensus size: 50
713781 ATTTATTACA
*
713791 AATTTT-AAATATAATAAATAATATTATTTATGATAAAACTTAGTATTAT
1 AATTTTAAAATATAATAAATAATATTATTTATGATAAAACTTACTATTAT
* * * *
713840 TATTTTAAAATATTA-AAATAAT-TTATTTATTATTAAATA-TTACTTTTAT
1 AATTTTAAAATATAATAAATAATATTATTTATGA-TAAA-ACTTACTATTAT
713889 AATTTTA
1 AATTTTA
713896 TTAATAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
48 9 0.19
49 30 0.64
50 8 0.17
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (50 bp):
AATTTTAAAATATAATAAATAATATTATTTATGATAAAACTTACTATTAT
Found at i:714154 original size:14 final size:14
Alignment explanation
Indices: 714135--714183 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
714125 TGATTATTTT
714135 ATATAATATTAAAA
1 ATATAATATTAAAA
**
714149 ATATAATATTATTA
1 ATATAATATTAAAA
*
714163 TTATAAATATTAATAA
1 ATAT-AATATTAA-AA
714179 ATATA
1 ATATA
714184 TTTAAATATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 15 0.56
15 8 0.30
16 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATAATATTAAAA
Found at i:714161 original size:29 final size:32
Alignment explanation
Indices: 714107--714183 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 32
714097 ATAATATCTT
*
714107 ATATTATTATAATATAATTGATTATT-TTATATA
1 ATATTAATA-AATATAATTGATTATTATTATA-A
714140 ATATTAA-AAATATAA-T-ATTATTATTATAA
1 ATATTAATAAATATAATTGATTATTATTATAA
714169 ATATTAATAAATATA
1 ATATTAATAAATATA
714184 TTTAAATATT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 14 0.34
30 13 0.32
31 7 0.17
32 1 0.02
33 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
ATATTAATAAATATAATTGATTATTATTATAA
Found at i:714193 original size:29 final size:30
Alignment explanation
Indices: 714107--714183 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 30
714097 ATAATATCTT
* *
714107 ATATTATTATAATATAATTGATT-ATTTTATATA
1 ATATTAATA-AATATAA-T-ATTAATATTATA-A
*
714140 ATATTAA-AAATATAATATTATTATTATAA
1 ATATTAATAAATATAATATTAATATTATAA
714169 ATATTAATAAATATA
1 ATATTAATAAATATA
714184 TTTAAATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 11 0.28
30 14 0.36
31 7 0.18
32 1 0.03
33 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (30 bp):
ATATTAATAAATATAATATTAATATTATAA
Found at i:714486 original size:39 final size:40
Alignment explanation
Indices: 714379--714491 Score: 156
Period size: 42 Copynumber: 2.8 Consensus size: 40
714369 ATGAATTACG
*
714379 TTCCGGAAAACGAATTATGTGAAACAAACACTGGAAAATATT
1 TTCC-GAAAACGAATTACGTGAAACAAACAC-GGAAAATATT
*
714421 TTCCGAAAAACGAATTACGTGCAACAAACACGGAAAA-ATT
1 TTCCG-AAAACGAATTACGTGAAACAAACACGGAAAATATT
* *
714461 TTTCGAAAACGAATTACATGAAACAAACACG
1 TTCCGAAAACGAATTACGTGAAACAAACACG
714492 AAATTTCGGA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
39 24 0.37
40 7 0.11
41 7 0.11
42 27 0.42
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (40 bp):
TTCCGAAAACGAATTACGTGAAACAAACACGGAAAATATT
Found at i:721488 original size:24 final size:24
Alignment explanation
Indices: 721461--721565 Score: 106
Period size: 24 Copynumber: 4.4 Consensus size: 24
721451 AAACGGAGAT
* *
721461 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
721485 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
721509 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
721533 GTAATG-TATCAGAACAGAATTCA-
1 ATCA-GAAATCAGAACAGAATTCAG
721556 AGTCAGAAAT
1 A-TCAGAAAT
721566 TAGATAAAAT
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
23 1 0.02
24 63 0.97
25 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:721532 original size:12 final size:12
Alignment explanation
Indices: 721473--721532 Score: 59
Period size: 12 Copynumber: 5.0 Consensus size: 12
721463 CATAAATCAA
721473 AACAGAATTCAG
1 AACAGAATTCAG
* *
721485 ATCAG-ATATCAT
1 AACAGAAT-TCAG
*
721497 AACAGAATCCAG
1 AACAGAATTCAG
* *
721509 ATCAGAAATCAG
1 AACAGAATTCAG
721521 AACAGAATTCAG
1 AACAGAATTCAG
721533 GTAATGTATC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
11 2 0.06
12 32 0.89
13 2 0.06
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:721543 original size:48 final size:47
Alignment explanation
Indices: 721461--721565 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 47
721451 AAACGGAGAT
* * *
721461 ATCATAAATCAAAACAGAATTCAGATCAGATATCATAACAGAATCCA
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCA
* * *
721508 GATCAGAAATCAGAACAGAATTCAGGTAATG-TATCAGAACAGAATTCA
1 -ATCAGAAATCAAAACAGAATTCAGATAA-GATATCAGAACAGAATCCA
721556 AGTCAGAAAT
1 A-TCAGAAAT
721566 TAGATAAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 1 0.02
48 47 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.21
Consensus pattern (47 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCA
Found at i:726136 original size:24 final size:24
Alignment explanation
Indices: 726109--726204 Score: 138
Period size: 24 Copynumber: 4.0 Consensus size: 24
726099 AAACGGAGAT
726109 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
726133 ATCAGATATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
726157 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
726181 ATCAGAAATCAGAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
726205 GTAATGTATC
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:726138 original size:12 final size:12
Alignment explanation
Indices: 726111--726204 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
726101 ACGGAGATAT
* *
726111 CAGAAATCAAAA
1 CAGAATTCAGAA
*
726123 CAGAATTCAGAT
1 CAGAATTCAGAA
*
726135 CAG-ATATCAAAA
1 CAGAAT-TCAGAA
*
726147 CAGAATTCAGAT
1 CAGAATTCAGAA
*
726159 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* *
726171 CAGAATCCAGAT
1 CAGAATTCAGAA
*
726183 CAGAAATCAGAA
1 CAGAATTCAGAA
*
726195 CATAATTCAG
1 CAGAATTCAG
726205 GTAATGTATC
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 4 0.07
12 53 0.87
13 4 0.07
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:726215 original size:48 final size:48
Alignment explanation
Indices: 726116--726241 Score: 139
Period size: 48 Copynumber: 2.6 Consensus size: 48
726106 GATATCAGAA
* *
726116 ATCAAAACAGAATTCAGATCAGATATCAAAACAGAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAAATCAAAACAGAATTCAGATAAGAT
* * * * *
726164 ATCATAACAGAATCCAGATCAGAAATCAGAACATAATTCAGGTAATG-T
1 ATCAAAACAGAATTCAGATCAGAAATCAAAACAGAATTCAGATAA-GAT
* *
726212 ATCAGAACATAATTCA-AGTCAGAAATCAAA
1 ATCAAAACAGAATTCAGA-TCAGAAATCAAA
726242 TAAAATATTT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
47 1 0.02
48 63 0.97
49 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAAAACAGAATTCAGATCAGAAATCAAAACAGAATTCAGATAAGAT
Found at i:728646 original size:10 final size:10
Alignment explanation
Indices: 728624--728692 Score: 50
Period size: 10 Copynumber: 6.5 Consensus size: 10
728614 CAACGGTTGT
728624 TCAACGCTCGG
1 TCAACG-TCGG
728635 TCAACGTCGG
1 TCAACGTCGG
*
728645 TCAAAGTTCAGG
1 TCAACG-TC-GG
728657 TCAACTGT-GG
1 TCAAC-GTCGG
* *
728667 TCAACGCCTG
1 TCAACGTCGG
*
728677 TCAACGGTCAG
1 TCAAC-GTCGG
728688 TCAAC
1 TCAAC
728693 AGTTTTACAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
9 1 0.02
10 22 0.47
11 16 0.34
12 7 0.15
13 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.22
Consensus pattern (10 bp):
TCAACGTCGG
Found at i:729000 original size:24 final size:23
Alignment explanation
Indices: 728970--729055 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 23
728960 AATTTGAACG
728970 ACCGGTTTTTTTACCGGATTAAAA
1 ACCGGTTTTTTTACCGGA-TAAAA
*
728994 ACTGGTTTTTTTCAAACCGGATAAAAA
1 ACCGGTTTTTTT---ACCGGAT-AAAA
*
729021 ACCGGTTTTTAT-CCGGA-AAAA
1 ACCGGTTTTTTTACCGGATAAAA
729042 ATCCGGTTTTTTTA
1 A-CCGGTTTTTTTA
729056 AAAAACTGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
21 5 0.10
22 10 0.19
23 5 0.10
24 11 0.21
26 1 0.02
27 20 0.38
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (23 bp):
ACCGGTTTTTTTACCGGATAAAA
Found at i:729042 original size:23 final size:22
Alignment explanation
Indices: 729010--729052 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
729000 TTTTTTCAAA
729010 CCGGATAAAAAACCGGTTTTTAT
1 CCGGA-AAAAAACCGGTTTTTAT
*
729033 CCGGAAAAAATCCGGTTTTT
1 CCGGAAAAAAACCGGTTTTT
729053 TTAAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (22 bp):
CCGGAAAAAAACCGGTTTTTAT
Found at i:729047 original size:22 final size:21
Alignment explanation
Indices: 729016--729091 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
729006 CAAACCGGAT
729016 AAAAAA-CCGGTTTTTATCCGG
1 AAAAAATCCGGTTTTTATCC-G
*
729037 AAAAAATCCGGTTTTT-T--T
1 AAAAAATCCGGTTTTTATCCG
*
729055 AAAAAA-CTGGATTTTTATCCG
1 AAAAAATCCGG-TTTTTATCCG
*
729076 AAAAAATCTGGTTTTT
1 AAAAAATCCGGTTTTT
729092 TTTAAAAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
17 3 0.07
18 11 0.24
19 1 0.02
21 18 0.39
22 13 0.28
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (21 bp):
AAAAAATCCGGTTTTTATCCG
Found at i:729110 original size:40 final size:39
Alignment explanation
Indices: 729015--729109 Score: 147
Period size: 39 Copynumber: 2.4 Consensus size: 39
729005 TCAAACCGGA
729015 TAAAAAACCGGTTTTTATCCGGAAAAAATCCGGTTTTTT
1 TAAAAAACCGGTTTTTATCCGGAAAAAATCCGGTTTTTT
* *
729054 TAAAAAACTGGATTTTTATCC-GAAAAAATCTGGTTTTTTT
1 TAAAAAACCGG-TTTTTATCCGGAAAAAATCCGG-TTTTTT
729094 TAAAAAACCGGTTTTT
1 TAAAAAACCGGTTTTT
729110 TTACAAACCG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
39 26 0.51
40 25 0.49
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.39
Consensus pattern (39 bp):
TAAAAAACCGGTTTTTATCCGGAAAAAATCCGGTTTTTT
Found at i:729119 original size:16 final size:17
Alignment explanation
Indices: 729037--729112 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 17
729027 TTTTATCCGG
729037 AAAAAATCCGGTTTTTTT
1 AAAAAA-CCGGTTTTTTT
* *
729055 AAAAAACTGGATTTTTATCCG
1 AAAAAACCGG-TTTTT-T--T
*
729076 AAAAAATCTGGTTTTTTTT
1 AAAAAA-CCGG-TTTTTTT
729095 AAAAAACCGGTTTTTTT
1 AAAAAACCGGTTTTTTT
729112 A
1 A
729113 CAAACCGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
17 11 0.23
18 14 0.29
19 7 0.15
21 7 0.15
22 9 0.19
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (17 bp):
AAAAAACCGGTTTTTTT
Found at i:732021 original size:31 final size:31
Alignment explanation
Indices: 731984--732050 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
731974 TATAATACAA
*
731984 TCCCCCAACATTTAATAT-ATTTGCAATATGG
1 TCCCCCAACATTTAAT-TCATTTACAATATGG
* * *
732015 TCCCCCAATATTTAGTTCGTTTACAATATGG
1 TCCCCCAACATTTAATTCATTTACAATATGG
732046 TCCCC
1 TCCCC
732051 GACGTAATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TCCCCCAACATTTAATTCATTTACAATATGG
Found at i:734353 original size:31 final size:31
Alignment explanation
Indices: 734315--734382 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
734305 CAGTTACGCC
734315 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
734346 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCATATTGCAAACGGACTAAATGTTG
734377 GGGGAC
1 GGGGAC
734383 TGGATTGCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.16, G:0.32, T:0.21
Consensus pattern (31 bp):
GGGGACCATATTGCAAACGGACTAAATGTTG
Found at i:734390 original size:31 final size:31
Alignment explanation
Indices: 734315--734392 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
734305 CAGTTACGCC
*
734315 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCAGATTGCAAACGGACTAAATGTTG
*
734346 GGGGACCATATTGCAAACGGACTAAATGTTG
1 GGGGACCAGATTGCAAACGGACTAAATGTTG
**
734377 GGGGACTGGATTGCAA
1 GGGGACCAGATTGCAA
734393 GTTTTAAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (31 bp):
GGGGACCAGATTGCAAACGGACTAAATGTTG
Found at i:735888 original size:3 final size:3
Alignment explanation
Indices: 735882--735923 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
735872 ATAATACAAT
735882 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
735924 AATTCTTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:736330 original size:17 final size:17
Alignment explanation
Indices: 736308--736342 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
736298 CTATCTTAAA
736308 ATTTTAAA-ATTTTATAT
1 ATTTTAAATATTTT-TAT
736325 ATTTTAAATATTTTTAT
1 ATTTTAAATATTTTTAT
736342 A
1 A
736343 AATAATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTAAATATTTTTAT
Found at i:744087 original size:64 final size:64
Alignment explanation
Indices: 744019--744173 Score: 174
Period size: 64 Copynumber: 2.4 Consensus size: 64
744009 TTGAAGGTGT
* ** *
744019 ATCGATGCACAAGTAGTGCATCGATGTA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACAAGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
744081 GC
63 GC
* * *
744083 ATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCACAA-GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
*
744147 ACCGATGCACAAGTAGTGCATCGATGC
1 ATCGATGCACAAGTAGTGCATCGATGC
744174 TTACCTTCAT
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
63 2 0.03
64 65 0.86
65 9 0.12
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:745193 original size:21 final size:21
Alignment explanation
Indices: 745168--745208 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
745158 TCTGGGCAAA
* *
745168 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
745189 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
745209 ACGACAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:745278 original size:23 final size:22
Alignment explanation
Indices: 745234--745278 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
745224 AATGCCAGAG
*
745234 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
745256 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
745279 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:749020 original size:21 final size:21
Alignment explanation
Indices: 748995--749035 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
748985 TCTGGGCAAA
* *
748995 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
749016 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
749036 ACGACAGAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:749901 original size:29 final size:29
Alignment explanation
Indices: 749859--749968 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
749849 TATGTGATAT
*
749859 GAGAACATAACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
749889 GAGAAATGACATGAGCTATATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
749918 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
749947 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
749969 ACATATAAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
28 7 0.09
29 63 0.84
30 5 0.07
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.18
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:750202 original size:16 final size:16
Alignment explanation
Indices: 750170--750203 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
750160 AGCATTAGTG
750170 CACAACCTCTATGTCT
1 CACAACCTCTATGTCT
750186 CACATACCTCTAT-TCT
1 CACA-ACCTCTATGTCT
750202 CA
1 CA
750204 ATAATATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.26, C:0.38, G:0.03, T:0.32
Consensus pattern (16 bp):
CACAACCTCTATGTCT
Found at i:750375 original size:22 final size:22
Alignment explanation
Indices: 750343--750392 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
750333 GTAAGAATGC
750343 ATTCATAAAGATATTGTTGCAT
1 ATTCATAAAGATATTGTTGCAT
*
750365 ATTCATGAAGATATTGTTGCAT
1 ATTCATAAAGATATTGTTGCAT
750387 ATTCAT
1 ATTCAT
750393 TTATTGCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (22 bp):
ATTCATAAAGATATTGTTGCAT
Found at i:754583 original size:51 final size:51
Alignment explanation
Indices: 754523--754626 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
754513 TAGTATGATC
**
754523 TTATGTTTCCCTAGGAAGGTGAAATATGAGTTGTTTCAAAGACTACCAAGG
1 TTATGTTTCCCTAGGAAGGTGAAATATGAGTTGTGACAAAGACTACCAAGG
* *
754574 TTATGTTTCCCTAGGAAGGTTAAATATGAGTTGTGACAAAGATTACCAAGG
1 TTATGTTTCCCTAGGAAGGTGAAATATGAGTTGTGACAAAGACTACCAAGG
754625 TT
1 TT
754627 CATCTATTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (51 bp):
TTATGTTTCCCTAGGAAGGTGAAATATGAGTTGTGACAAAGACTACCAAGG
Found at i:755779 original size:23 final size:23
Alignment explanation
Indices: 755753--755827 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
755743 ATATCATCGA
*
755753 AGTGTCGCGTAGAAATGCACCGT
1 AGTGCCGCGTAGAAATGCACCGT
* * *
755776 AGTGCCACGTAGAATTGCACCGA
1 AGTGCCGCGTAGAAATGCACCGT
* *
755799 AGTGGCGTGTAGAAATGCACCGT
1 AGTGCCGCGTAGAAATGCACCGT
755822 AGTGCC
1 AGTGCC
755828 ATATAATGTC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.27, C:0.23, G:0.31, T:0.20
Consensus pattern (23 bp):
AGTGCCGCGTAGAAATGCACCGT
Found at i:757446 original size:19 final size:19
Alignment explanation
Indices: 757422--757458 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
757412 TTTAAGGGGG
*
757422 TGCATCGATGCACTACTTA
1 TGCATCGATACACTACTTA
757441 TGCATCGATACACTACTT
1 TGCATCGATACACTACTT
757459 GCATTCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (19 bp):
TGCATCGATACACTACTTA
Done.