Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 31 of 31
Found at i:14187431 original size:2 final size:2
Alignment explanation
Indices: 14187424--14187458 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
14187414 AGCAACAGGC
*
14187424 TA TA TA TA AA 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 T
14187459 GTGTGTGTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14188035 original size:20 final size:20
Alignment explanation
Indices: 14187999--14188037 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
14187989 ATTGCATTTC
*
14187999 TTTAAAAAATATCCAAAAAT
1 TTTAAAAAATATACAAAAAT
*
14188019 TTTAAAAAATTTACAAAAA
1 TTTAAAAAATATACAAAAA
14188038 CAAAGTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (20 bp):
TTTAAAAAATATACAAAAAT
Found at i:14190485 original size:21 final size:21
Alignment explanation
Indices: 14190461--14190509 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
14190451 TACTTAAAGT
14190461 AAATTAAAAC-AAAATAACATA
1 AAATTAAAACTAAAATAAC-TA
*
14190482 AAATT-AAACTAAAATAACTT
1 AAATTAAAACTAAAATAACTA
14190502 AAATTAAA
1 AAATTAAA
14190510 CTACTCAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (21 bp):
AAATTAAAACTAAAATAACTA
Found at i:14190490 original size:20 final size:20
Alignment explanation
Indices: 14190461--14190512 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
14190451 TACTTAAAGT
14190461 AAATTAAAAC-AAAATAACATA
1 AAATT-AAACTAAAATAAC-TA
*
14190482 AAATTAAACTAAAATAACTT
1 AAATTAAACTAAAATAACTA
14190502 AAATTAAACTA
1 AAATTAAACTA
14190513 CTCAGCATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATTAAACTAAAATAACTA
Found at i:14195660 original size:21 final size:21
Alignment explanation
Indices: 14195635--14195679 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
14195625 ATTCCATATT
14195635 CTTGCTTATGGATGTTTATAC
1 CTTGCTTATGGATGTTTATAC
14195656 CTTGCTTATGGATGTTTATAC
1 CTTGCTTATGGATGTTTATAC
14195677 CTT
1 CTT
14195680 CATGAACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.49
Consensus pattern (21 bp):
CTTGCTTATGGATGTTTATAC
Found at i:14196511 original size:25 final size:25
Alignment explanation
Indices: 14196478--14196529 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
14196468 AAAGCTTTTC
14196478 AAAACATTGAGTCTTCAATTGAGTA
1 AAAACATTGAGTCTTCAATTGAGTA
14196503 AAAACATTGAGTCTTCAATTGAGTA
1 AAAACATTGAGTCTTCAATTGAGTA
14196528 AA
1 AA
14196530 TATAGAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (25 bp):
AAAACATTGAGTCTTCAATTGAGTA
Found at i:14198947 original size:28 final size:27
Alignment explanation
Indices: 14198893--14199062 Score: 119
Period size: 28 Copynumber: 6.0 Consensus size: 27
14198883 TTAAAACGAC
* * *
14198893 TCTTGTCTTTAATTAAGATAAACATGTT
1 TCTTGTC-TAAATTAAGACAAATATGTT
*
14198921 ATCTTGTCTAAATTGAGACAAATATGTT
1 -TCTTGTCTAAATTAAGACAAATATGTT
* * * *
14198949 TTTTGGTC-AAGATTAAAATAAAACATATTTT
1 TCTT-GTCTAA-ATT--AAGACAA-ATATGTT
* * *
14198980 TCTTGTCTTAAATTAATAGACATAT-TT
1 TCTTGTC-TAAATTAAGACAAATATGTT
* *
14199007 TCTTGTCTATATTAAGACAAAACATGTTT
1 TCTTGTCTAAATTAAGAC-AAATATG-TT
14199036 TCTTGTCTAAATTAAGACAAATATGTT
1 TCTTGTCTAAATTAAGACAAATATGTT
14199063 GAAGCTGACA
Statistics
Matches: 112, Mismatches: 19, Indels: 22
0.73 0.12 0.14
Matches are distributed among these distances:
26 8 0.07
27 20 0.18
28 32 0.29
29 31 0.28
30 7 0.06
31 12 0.11
32 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (27 bp):
TCTTGTCTAAATTAAGACAAATATGTT
Found at i:14198991 original size:26 final size:27
Alignment explanation
Indices: 14198961--14199014 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
14198951 TTGGTCAAGA
14198961 TTAAAATAA-A-ACATATTTTTCTTGTC
1 TTAAAATAATAGACATA-TTTTCTTGTC
*
14198987 TTAAATTAATAGACATATTTTCTTGTC
1 TTAAAATAATAGACATATTTTCTTGTC
14199014 T
1 T
14199015 ATATTAAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 12 0.48
28 5 0.20
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (27 bp):
TTAAAATAATAGACATATTTTCTTGTC
Found at i:14199051 original size:29 final size:29
Alignment explanation
Indices: 14198893--14199056 Score: 126
Period size: 29 Copynumber: 5.7 Consensus size: 29
14198883 TTAAAACGAC
* * *
14198893 TCTTGTCTTTAATTAAGA-TAAACATGTTA
1 TCTTGTC-TAAATTAAGACAAAACATGTTT
* *
14198922 TCTTGTCTAAATTGAGAC-AAATATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
* * *
14198950 T-TTGGTC-AAGATTAAAATAAAACATATTTT
1 TCTT-GTCTAA-ATTAAGACAAAACAT-GTTT
* * *
14198980 TCTTGTCTTAAATT-A-A-TAGACATATTT
1 TCTTGTC-TAAATTAAGACAAAACATGTTT
*
14199007 TCTTGTCTATATTAAGACAAAACATGTTT
1 TCTTGTCTAAATTAAGACAAAACATGTTT
14199036 TCTTGTCTAAATTAAGACAAA
1 TCTTGTCTAAATTAAGACAAA
14199057 TATGTTGAAG
Statistics
Matches: 107, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
26 5 0.05
27 15 0.14
28 31 0.29
29 41 0.38
30 8 0.07
31 5 0.05
32 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.42
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAACATGTTT
Found at i:14201908 original size:16 final size:16
Alignment explanation
Indices: 14201889--14201919 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14201879 ACTATAATTC
14201889 TTTTTA-TCTTTATTT
1 TTTTTATTCTTTATTT
14201904 TTTTTATTCTTTATTT
1 TTTTTATTCTTTATTT
14201920 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTATTCTTTATTT
Found at i:14202492 original size:241 final size:241
Alignment explanation
Indices: 14202040--14202496 Score: 738
Period size: 241 Copynumber: 1.9 Consensus size: 241
14202030 NNNNNNNNNN
* *
14202040 AAAATTTTTATATCGTTAAACACTTTCAGCCTAAGAATATAAATTTAAATATTTACTTTTGATTT
1 AAAATTTTTATATCGTTAAACACTTTCAGCCCAAGAATATAAATTTAAATATTTACTTTTGATTA
* *
14202105 AATTTATATTGTTTTTACTTAATTTATTTTTTACGTTAACTCTCACACGCTTACGTTAAGATTTA
66 AATTTATATTGTTTTTACTTAATTGATTTTTTACGTTAACTCTCACACGCTTACGCTAAGATTTA
* * *
14202170 AAATTTAGTTATTTCGCCTTTACAAGCTCTTATGTCAATTCTTATAGTTTTACGTCAAGGCTTTT
131 AAATTTAGTTATTCCACCTTTACAAGCTCTTATGTCAATTCTTATAGTTTTACGTCAAGCCTTTT
* ** *
14202235 GCATGTCAATTTTAAATTATAATTAGTTATCATTTATTTAAAAATT
196 GAATAACAACTTTAAATTATAATTAGTTATCATTTATTTAAAAATT
* * *
14202281 AAAATTTTTATATCGTTAAACACTTTCAGCCCGAGAATATAAATTTAAATTTTTTCTTTTGATTA
1 AAAATTTTTATATCGTTAAACACTTTCAGCCCAAGAATATAAATTTAAATATTTACTTTTGATTA
*
14202346 AATTTATATTGTTTTTACTTAATTGATTTTTTACGTTAACTCTCACACGCTTACGCTAATATTTA
66 AATTTATATTGTTTTTACTTAATTGATTTTTTACGTTAACTCTCACACGCTTACGCTAAGATTTA
*
14202411 AAATTTAGTTATTCCACCTTTACAAGCTTTTATGTCAATTCTTACT-GTTTTACGTCAAGACCTT
131 AAATTTAGTTATTCCACCTTTACAAGCTCTTATGTCAATTCTTA-TAGTTTTACGTCAAG-CCTT
14202475 TT-AATAACAACTTTAAATTATA
194 TTGAATAACAACTTTAAATTATA
14202497 TGTTTTTTTA
Statistics
Matches: 198, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
241 192 0.97
242 6 0.03
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (241 bp):
AAAATTTTTATATCGTTAAACACTTTCAGCCCAAGAATATAAATTTAAATATTTACTTTTGATTA
AATTTATATTGTTTTTACTTAATTGATTTTTTACGTTAACTCTCACACGCTTACGCTAAGATTTA
AAATTTAGTTATTCCACCTTTACAAGCTCTTATGTCAATTCTTATAGTTTTACGTCAAGCCTTTT
GAATAACAACTTTAAATTATAATTAGTTATCATTTATTTAAAAATT
Found at i:14206325 original size:62 final size:61
Alignment explanation
Indices: 14206236--14206443 Score: 226
Period size: 62 Copynumber: 3.4 Consensus size: 61
14206226 CATTCACAGG
14206236 GCAGTAGCATCAACACTGCAGCGCCACACTCCCAGTGCTGCAGCGCTGTGCCCCTTCACCAA
1 GCAGTAGCATCAACACTGCAGCGCCACACTCCCAGTGCTGCAGCGCTGT-CCCCTTCACCAA
* * * ** * *
14206298 GTAGTAGCATCAACGCTGCAACGCCACACTCCCAGCACTGCAGCACTGTCCCATTCACCAA
1 GCAGTAGCATCAACACTGCAGCGCCACACTCCCAGTGCTGCAGCGCTGTCCCCTTCACCAA
* * * *
14206359 GCA--A-CACTCCCAGCACTGTAGCGCCACACTCCCAGTGCTGCAACGTTGTCCCCCTTCA-CAA
1 GCAGTAGCA-T--CAACACTGCAGCGCCACACTCCCAGTGCTGCAGCGCTGT-CCCCTTCACCAA
*
14206420 GGCAGTAGCATCAACGCTGCAGCG
1 -GCAGTAGCATCAACACTGCAGCG
14206444 TTGTGCCCCT
Statistics
Matches: 117, Mismatches: 21, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
58 2 0.02
59 2 0.02
61 46 0.39
62 63 0.54
64 2 0.02
65 2 0.02
ACGTcount: A:0.25, C:0.39, G:0.20, T:0.16
Consensus pattern (61 bp):
GCAGTAGCATCAACACTGCAGCGCCACACTCCCAGTGCTGCAGCGCTGTCCCCTTCACCAA
Found at i:14206439 original size:40 final size:40
Alignment explanation
Indices: 14206395--14206477 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
14206385 CACTCCCAGT
*
14206395 GCTGCAACGTTGTCCCCCTTCA-CAAGGCAGTAGCATCAAC
1 GCTGCAACGTTGTCCCCCTTCACCAA-GAAGTAGCATCAAC
* *
14206435 GCTGCAGCGTTGTGCCCCTTCACCAAGAAGTAGCATCAAC
1 GCTGCAACGTTGTCCCCCTTCACCAAGAAGTAGCATCAAC
14206475 GCT
1 GCT
14206478 TCAGCACCAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
40 36 0.92
41 3 0.08
ACGTcount: A:0.24, C:0.34, G:0.22, T:0.20
Consensus pattern (40 bp):
GCTGCAACGTTGTCCCCCTTCACCAAGAAGTAGCATCAAC
Found at i:14206550 original size:163 final size:163
Alignment explanation
Indices: 14206272--14206601 Score: 453
Period size: 163 Copynumber: 2.0 Consensus size: 163
14206262 CACTCCCAGT
* *
14206272 GCTGCAGCGCTGTGCCCCTTCACCAAGTAGTAGCATCAACGCTGCAACGCCACACTCCCAGCACT
1 GCTGCAGCGCTGTGCCCCTTCACCAAGAAGTAGCATCAACGCTGCAACACCACACTCCCAGCACT
* **
14206337 GCAGCACTGTCCCATTCACCAAGCAACACTCCCAGCACTGTAGCGCCACACTCCCAGTGCTGCAA
66 GCAGCACTGTCCCATTCACCAAGCAACACTCCCAGCACTGCAGCGCCACACTCCCAGCACTGCAA
*
14206402 CGTTGTCCCCCTTCACAAGGCAGTAGCATCAAC
131 CGCTGTCCCCCTTCACAAGGCAGTAGCATCAAC
* * * * *
14206435 GCTGCAGCGTTGTGCCCCTTCACCAAGAAGTAGCATCAACGCTTCAGCACCACATTCCCAGCGCT
1 GCTGCAGCGCTGTGCCCCTTCACCAAGAAGTAGCATCAACGCTGCAACACCACACTCCCAGCACT
* * * * ** * ** *
14206500 GTAGCGCTGTCCCATTCACCAAGCAGCACTCCTAGTGCTGCAGTGCCACACTCTTAGCACTGCAG
66 GCAGCACTGTCCCATTCACCAAGCAACACTCCCAGCACTGCAGCGCCACACTCCCAGCACTGCAA
* *
14206565 CGCTGTCCCCCTTCATAAGGCAGTAGCATCAAT
131 CGCTGTCCCCCTTCACAAGGCAGTAGCATCAAC
14206598 GCTG
1 GCTG
14206602 TATCACCACA
Statistics
Matches: 144, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
163 144 1.00
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.19
Consensus pattern (163 bp):
GCTGCAGCGCTGTGCCCCTTCACCAAGAAGTAGCATCAACGCTGCAACACCACACTCCCAGCACT
GCAGCACTGTCCCATTCACCAAGCAACACTCCCAGCACTGCAGCGCCACACTCCCAGCACTGCAA
CGCTGTCCCCCTTCACAAGGCAGTAGCATCAAC
Found at i:14206612 original size:62 final size:62
Alignment explanation
Indices: 14206449--14206820 Score: 297
Period size: 62 Copynumber: 6.0 Consensus size: 62
14206439 CAGCGTTGTG
* * * * * * * *
14206449 CCCCTTCACCAA-GAAGTAGCATCAACGCTTCAGCACCACATTCCCAGCGCTGTAGCGCTGT-
1 CCCCTTCA-CAAGGCAGTAGCATCAATGCTGCAGCACCACACTCCTAGCACTGCAGCGCTATC
* * * ** * *
14206510 CCCATTCACCAA-GCAGCA-C-TCCTAGTGCTGCAGTGCCACACTCTTAGCACTGCAGCGCTGTC
1 CCCCTTCA-CAAGGCAGTAGCAT-C-AATGCTGCAGCACCACACTCCTAGCACTGCAGCGCTATC
* * * * ** *
14206572 CCCCTTCATAAGGCAGTAGCATCAATGCTGTATCACCACACTCCCAGTGCTGCAGCGCTATG
1 CCCCTTCACAAGGCAGTAGCATCAATGCTGCAGCACCACACTCCTAGCACTGCAGCGCTATC
* * *
14206634 CCCCTTCACCAA-GTAGTAGCATCAATGCTGCAGCGCCACACTCCTAGCACTGCAGTGCTATC
1 CCCCTTCA-CAAGGCAGTAGCATCAATGCTGCAGCACCACACTCCTAGCACTGCAGCGCTATC
* * ** * * ** *
14206696 CCCCTTCACAAGGCAATAGCATCAAAGCTATAGCGCCACACTCCCAGTGCTGCAGCGCTGTC
1 CCCCTTCACAAGGCAGTAGCATCAATGCTGCAGCACCACACTCCTAGCACTGCAGCGCTATC
* * * * * *
14206758 CTCCTTCACAAGGCAGTAGCATCAACGCTGCAGAACCACACTCCTAGCATTACAGCACTATC
1 CCCCTTCACAAGGCAGTAGCATCAATGCTGCAGCACCACACTCCTAGCACTGCAGCGCTATC
14206820 C
1 C
14206821 TTTTCACCAA
Statistics
Matches: 242, Mismatches: 61, Indels: 15
0.76 0.19 0.05
Matches are distributed among these distances:
59 1 0.00
60 2 0.01
61 48 0.20
62 186 0.77
63 4 0.02
64 1 0.00
ACGTcount: A:0.25, C:0.37, G:0.18, T:0.20
Consensus pattern (62 bp):
CCCCTTCACAAGGCAGTAGCATCAATGCTGCAGCACCACACTCCTAGCACTGCAGCGCTATC
Found at i:14206698 original size:124 final size:124
Alignment explanation
Indices: 14206535--14206820 Score: 378
Period size: 124 Copynumber: 2.3 Consensus size: 124
14206525 GCACTCCTAG
* * * * * *
14206535 TGCTGCAGTGCCACACTCTTAGCACTGCAGCGCTGTCCCCCTTCATAAGGCAGTAGCATCAATGC
1 TGCTGCAGAGCCACACTCCTAGCACTGCAGCGCTATCCCCCTTCACAAGGCAATAGCATCAAAGC
* * *
14206600 TGTATCACCACACTCCCAGTGCTGCAGCGCTATGCC-CCTTCACCAA-GTAGTAGCATCAA
66 TATAGCACCACACTCCCAGTGCTGCAGCGCTAT-CCTCCTTCA-CAAGGCAGTAGCATCAA
* *
14206659 TGCTGCAGCGCCACACTCCTAGCACTGCAGTGCTATCCCCCTTCACAAGGCAATAGCATCAAAGC
1 TGCTGCAGAGCCACACTCCTAGCACTGCAGCGCTATCCCCCTTCACAAGGCAATAGCATCAAAGC
* *
14206724 TATAGCGCCACACTCCCAGTGCTGCAGCGCTGTCCTCCTTCACAAGGCAGTAGCATCAA
66 TATAGCACCACACTCCCAGTGCTGCAGCGCTATCCTCCTTCACAAGGCAGTAGCATCAA
* * * * *
14206783 CGCTGCAGAACCACACTCCTAGCATTACAGCACTATCC
1 TGCTGCAGAGCCACACTCCTAGCACTGCAGCGCTATCC
14206821 TTTTCACCAA
Statistics
Matches: 141, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
123 5 0.04
124 136 0.96
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.21
Consensus pattern (124 bp):
TGCTGCAGAGCCACACTCCTAGCACTGCAGCGCTATCCCCCTTCACAAGGCAATAGCATCAAAGC
TATAGCACCACACTCCCAGTGCTGCAGCGCTATCCTCCTTCACAAGGCAGTAGCATCAA
Found at i:14206849 original size:61 final size:61
Alignment explanation
Indices: 14206784--14206912 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 61
14206774 TAGCATCAAC
* *
14206784 GCTGCAGAACCACACTCCTAGCATTACAGCACTATCCTTTTCACCAAGCAGCACTCCCAAT
1 GCTGCAGAACCACACTCCCAGCATTACAGCACTATCCCTTTCACCAAGCAGCACTCCCAAT
** ** * ** * *
14206845 GCTGCAGCGCCACACTCCCAGTGTTGCAGCGTTGTCCCTTTCACCAAGCAGCACTCCCAGT
1 GCTGCAGAACCACACTCCCAGCATTACAGCACTATCCCTTTCACCAAGCAGCACTCCCAAT
14206906 GCTGCAG
1 GCTGCAG
14206913 CGCTGTCCCC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.23, C:0.38, G:0.18, T:0.21
Consensus pattern (61 bp):
GCTGCAGAACCACACTCCCAGCATTACAGCACTATCCCTTTCACCAAGCAGCACTCCCAAT
Found at i:14209333 original size:26 final size:26
Alignment explanation
Indices: 14209304--14209362 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
14209294 TTTCATTAAT
*
14209304 TGACCTTCTAGTAAAGTCAAAAATAA
1 TGACCTTCCAGTAAAGTCAAAAATAA
*
14209330 TGACCTTCCAGTAAGGTCAAAAATAA
1 TGACCTTCCAGTAAAGTCAAAAATAA
14209356 TGACCTT
1 TGACCTT
14209363 ACTGCAGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (26 bp):
TGACCTTCCAGTAAAGTCAAAAATAA
Found at i:14210032 original size:18 final size:17
Alignment explanation
Indices: 14209995--14210027 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
14209985 TGAGCTATTC
14209995 CTTTCTCTCCTTATTTT
1 CTTTCTCTCCTTATTTT
*
14210012 CTTTTTCTCCTT-TTTT
1 CTTTCTCTCCTTATTTT
14210028 TTCTTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (17 bp):
CTTTCTCTCCTTATTTT
Found at i:14210251 original size:16 final size:17
Alignment explanation
Indices: 14210226--14210260 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
14210216 AAACAATAAT
*
14210226 AATAGTAAAT-AAAATA
1 AATAGAAAATAAAAATA
14210242 AATAGAAAATAAAAATA
1 AATAGAAAATAAAAATA
14210259 AA
1 AA
14210261 GTGAATAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (17 bp):
AATAGAAAATAAAAATA
Found at i:14213966 original size:21 final size:22
Alignment explanation
Indices: 14213933--14213976 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
14213923 AAGTGATTAA
14213933 TTTAAGTTATTTT-TGTTAAAT
1 TTTAAGTTATTTTGTGTTAAAT
* * *
14213954 TTTATGTTGTTTTGTTTTAAAT
1 TTTAAGTTATTTTGTGTTAAAT
14213976 T
1 T
14213977 ACTTTAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (22 bp):
TTTAAGTTATTTTGTGTTAAAT
Found at i:14218266 original size:16 final size:17
Alignment explanation
Indices: 14218245--14218277 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
14218235 TTCTAGACAA
14218245 TTAATT-AAAACTAAAT
1 TTAATTAAAAACTAAAT
14218261 TTAATTAGAAAACTAAA
1 TTAATTA-AAAACTAAA
14218278 ACTAATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (17 bp):
TTAATTAAAAACTAAAT
Found at i:14218283 original size:18 final size:18
Alignment explanation
Indices: 14218251--14218285 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14218241 ACAATTAATT
**
14218251 AAAACTAAATTTAATTAG
1 AAAACTAAAACTAATTAG
14218269 AAAACTAAAACTAATTA
1 AAAACTAAAACTAATTA
14218286 ATGAAGACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAACTAAAACTAATTAG
Found at i:14231327 original size:74 final size:74
Alignment explanation
Indices: 14231211--14231400 Score: 215
Period size: 74 Copynumber: 2.6 Consensus size: 74
14231201 TGAGACAGAG
* * * * *
14231211 AGAACTTAATTGACTAAGAAGCATGATTAATCAACTATGAGCTCACTGCC-AGAGACTTCAATTA
1 AGAACTTAA-TAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACT-CCTAGAGAATTCAATTA
*
14231275 CAAGACA-AAA
64 CAAAACACAAA
*
14231285 AGAACTTAATCAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTCCTAGCGAATTCAATTAC
1 AGAACTTAAT-AACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTCCTAGAGAATTCAATTAC
*
14231350 AAAACACAGA
65 AAAACACAAA
* * * *
14231360 AGAA-ATAATAGAGTAAGAAGTATGGTTAGTTAACTAAGAGC
1 AGAACTTAATA-ACTAAGAAGCATGGTTAGTCAACTAAGAGC
14231401 ATTCTGTCTG
Statistics
Matches: 100, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
73 4 0.04
74 90 0.90
75 6 0.06
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (74 bp):
AGAACTTAATAACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTCCTAGAGAATTCAATTACA
AAACACAAA
Found at i:14239682 original size:6 final size:6
Alignment explanation
Indices: 14239671--14239696 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
14239661 CTGAAGGTGA
14239671 TGAACC TGAACC TGAACC TGAACC TG
1 TGAACC TGAACC TGAACC TGAACC TG
14239697 CTCTAACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (6 bp):
TGAACC
Found at i:14241202 original size:74 final size:74
Alignment explanation
Indices: 14241108--14241380 Score: 420
Period size: 74 Copynumber: 3.7 Consensus size: 74
14241098 AGCAGATTGT
*
14241108 AAGATAAAGAGAACTTAATCGACTAAAAAGCATGGTTAGTCAACTTAGAGCTCACTGTCAGAGAC
1 AAGATAAAGAGAACTTAATCGACTAAAAAGCATGGTTAGTCAACTAAGAGCTCACTGTCAGAGAC
14241173 TTCAATTAC
66 TTCAATTAC
* *
14241182 AAGATAAAGAGAACTTAATCGATTAAAAAGCATGGTTAGTCAACTAAGAGCTCACTATCAGAGAC
1 AAGATAAAGAGAACTTAATCGACTAAAAAGCATGGTTAGTCAACTAAGAGCTCACTGTCAGAGAC
14241247 TTCAATTAC
66 TTCAATTAC
* * * * *
14241256 AAGATAAAGAGAACTTAATCGACTAAAAAGCATGGTTAGTTAACTAAAAGCTCACCGTTAGAGAA
1 AAGATAAAGAGAACTTAATCGACTAAAAAGCATGGTTAGTCAACTAAGAGCTCACTGTCAGAGAC
14241321 TTCAATTAC
66 TTCAATTAC
* * * * * *
14241330 AAGACAGAGAAAACTTAATCAACTAAGAAGTATGGTTAGTCAACTAAGAGC
1 AAGATAAAGAGAACTTAATCGACTAAAAAGCATGGTTAGTCAACTAAGAGC
14241381 ACTCTGTCTG
Statistics
Matches: 181, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 181 1.00
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (74 bp):
AAGATAAAGAGAACTTAATCGACTAAAAAGCATGGTTAGTCAACTAAGAGCTCACTGTCAGAGAC
TTCAATTAC
Found at i:14243244 original size:31 final size:29
Alignment explanation
Indices: 14243206--14243278 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 29
14243196 TGCTAGTTAT
14243206 TGTGGATATTCAATATATCTTGCTTAGCTAC
1 TGTGGATATT--ATATATCTTGCTTAGCTAC
* * *
14243237 TGTGGATATTGTATATCTTGTTTAGCTCC
1 TGTGGATATTATATATCTTGCTTAGCTAC
*
14243266 TATGGATATTATA
1 TGTGGATATTATA
14243279 AATATTTTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 27 0.73
31 10 0.27
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (29 bp):
TGTGGATATTATATATCTTGCTTAGCTAC
Found at i:14249581 original size:19 final size:19
Alignment explanation
Indices: 14249557--14249599 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
14249547 AAGTTTTCTC
* *
14249557 AATTAGTATCTAGCTTTAA
1 AATTAGCATCAAGCTTTAA
*
14249576 AATTAGCATCAAGCTTTAT
1 AATTAGCATCAAGCTTTAA
14249595 AATTA
1 AATTA
14249600 TCTCTTCTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (19 bp):
AATTAGCATCAAGCTTTAA
Found at i:14264726 original size:2 final size:2
Alignment explanation
Indices: 14264713--14264746 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
14264703 CAAGTCATAC
* *
14264713 GA GA GA GC GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
14264747 ACCACATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:14276323 original size:14 final size:15
Alignment explanation
Indices: 14276293--14276345 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 15
14276283 TAGGTATATT
14276293 ATTAATAAAAATAAA
1 ATTAATAAAAATAAA
*
14276308 ATTAAT-AAATTAAA
1 ATTAATAAAAATAAA
14276322 ATTAACTCATAAAATAAAA
1 ATTAA-T-A-AAAAT-AAA
14276341 ATTAA
1 ATTAA
14276346 AGTTTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 12 0.39
15 7 0.23
18 4 0.13
19 8 0.26
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAATAAAAATAAA
Found at i:14299581 original size:33 final size:32
Alignment explanation
Indices: 14299503--14299595 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 32
14299493 AATATATTTT
* *
14299503 TAATGTCATATATTTTATTTTTATTTATTATTA
1 TAATGTTATATATTTTA-TTTTATTTATTAATA
*
14299536 TAATGTTATATATTTTATTTTCATTTCTTTAATA
1 TAATGTTATATATTTTATTTT-ATTT-ATTAATA
* *
14299570 T-ATTTTTTATATTATATATTTTATTT
1 TAATGTTATATATT-T-TATTTTATTT
14299596 TAATTTGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
32 4 0.08
33 30 0.59
34 11 0.22
35 6 0.12
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (32 bp):
TAATGTTATATATTTTATTTTATTTATTAATA
Found at i:14302762 original size:71 final size:71
Alignment explanation
Indices: 14302669--14302840 Score: 197
Period size: 71 Copynumber: 2.4 Consensus size: 71
14302659 GGAAGTCATG
* *
14302669 CATTTTGGTCCAAGATCTACTATAGGCCCTTTATAGCCAATCCTATGAA-GAGAAAATG-G-AAG
1 CATTTTGGTCCAAGATCGACTATAGACCCTTTATAGCCAATCCTATGAAGGA-AAAATGAGTAA-
*
14302731 AAATGTAAA
64 AAA-GCAAA
* * * * * *
14302740 CATTTTGGTCCAAGATCGACTATTGACCTTTTATAGTCGATTCTGTGAAGGAAAAATGAGTAAAA
1 CATTTTGGTCCAAGATCGACTATAGACCCTTTATAGCCAATCCTATGAAGGAAAAATGAGTAAAA
14302805 AGCAAA
66 AGCAAA
* *
14302811 CATTCTAGTCCAAGATCGACTATAGACCCT
1 CATTTTGGTCCAAGATCGACTATAGACCCT
14302841 CCATAGTTGA
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
71 77 0.91
72 6 0.07
73 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (71 bp):
CATTTTGGTCCAAGATCGACTATAGACCCTTTATAGCCAATCCTATGAAGGAAAAATGAGTAAAA
AGCAAA
Found at i:14302847 original size:71 final size:71
Alignment explanation
Indices: 14302737--14302926 Score: 195
Period size: 71 Copynumber: 2.6 Consensus size: 71
14302727 GAAGAAATGT
* * * **
14302737 AAACATTTTGGTCCAAGATCGACTATTGACCTTTTATAGTCGAT-TCTGTGAAGGAAAAATGAGT
1 AAACATTCT-GTCCAAGATCGACTATAGACCCTCCATAGTCGATCT-TGTGAAGGAAAAATGAGT
14302801 AAAAAGC-
64 AAAAAGCA
* * * * *
14302808 AAACATTCTAGTCCAAGATCGACTATAGACCCTCCATAGTTGATCTTGTTAAGGAGAAATGGGTG
1 AAACATTCT-GTCCAAGATCGACTATAGACCCTCCATAGTCGATCTTGTGAAGGAAAAATGAGTA
*
14302873 AAACGCA
65 AAAAGCA
* ** *
14302880 AAACCTTCTGAAACAAGATCGACTATAGACCCTCCATAGTTGATCTT
1 AAACATTCTG-TCCAAGATCGACTATAGACCCTCCATAGTCGATCTT
14302927 AGATTGCCCA
Statistics
Matches: 101, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
71 58 0.57
72 43 0.43
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (71 bp):
AAACATTCTGTCCAAGATCGACTATAGACCCTCCATAGTCGATCTTGTGAAGGAAAAATGAGTAA
AAAGCA
Found at i:14304492 original size:63 final size:63
Alignment explanation
Indices: 14304433--14304552 Score: 204
Period size: 63 Copynumber: 1.9 Consensus size: 63
14304423 GTTTTCTTTG
* *
14304433 ACATCTTTTAAAAAGCTTTAAAGTCAATATTTTTAAATTGTTTTCTTAAAAATACTTTCTTCA
1 ACATCCTTTAAAAAGCTTTAAAGCCAATATTTTTAAATTGTTTTCTTAAAAATACTTTCTTCA
* *
14304496 ACATCCTTTACAAAGCTTTAAAGCCAATATTTTTAAATTGTTTTCTTGAAAATACTT
1 ACATCCTTTAAAAAGCTTTAAAGCCAATATTTTTAAATTGTTTTCTTAAAAATACTT
14304553 AAACGTTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (63 bp):
ACATCCTTTAAAAAGCTTTAAAGCCAATATTTTTAAATTGTTTTCTTAAAAATACTTTCTTCA
Found at i:14307190 original size:21 final size:20
Alignment explanation
Indices: 14307166--14307245 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 20
14307156 AATAATAAAC
*
14307166 AAATTAAATTGAA-TAAATATA
1 AAATTAAAAT-AACTAAATA-A
14307187 AAATTAAAATAACTAAATAA
1 AAATTAAAATAACTAAATAA
* *
14307207 AAA-TAAACTAATTAGAA-AA
1 AAATTAAAATAACTA-AATAA
*
14307226 ACAACTAAATATAACTAAAT
1 A-AATTAAA-ATAACTAAAT
14307246 TTTAGATAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
19 12 0.25
20 10 0.21
21 21 0.44
22 5 0.10
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATTAAAATAACTAAATAA
Found at i:14307208 original size:19 final size:19
Alignment explanation
Indices: 14307179--14307245 Score: 55
Period size: 19 Copynumber: 3.3 Consensus size: 19
14307169 TTAAATTGAA
14307179 TAAATATAAAATTAAAATAAC
1 TAAATA-AAAA-TAAAATAAC
* *
14307200 TAAATAAAAATAAACTAAT
1 TAAATAAAAATAAAATAAC
14307219 TAGAA-AAACAACTAAATATAAC
1 TA-AATAAA-AA-TAAA-ATAAC
14307241 TAAAT
1 TAAAT
14307246 TTTAGATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
19 12 0.32
20 8 0.22
21 12 0.32
22 5 0.14
ACGTcount: A:0.66, C:0.07, G:0.01, T:0.25
Consensus pattern (19 bp):
TAAATAAAAATAAAATAAC
Found at i:14309482 original size:2 final size:2
Alignment explanation
Indices: 14309477--14309511 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14309467 TCAAATATTG
14309477 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
14309512 GATCGTGTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:14321911 original size:21 final size:22
Alignment explanation
Indices: 14321876--14321919 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
14321866 CCTTTAAAGT
14321876 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
14321898 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
14321919 A
1 A
14321920 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:14327555 original size:47 final size:47
Alignment explanation
Indices: 14327495--14327614 Score: 195
Period size: 47 Copynumber: 2.6 Consensus size: 47
14327485 TTTTGCATAT
*
14327495 AATTTTACTTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
* * *
14327542 AATTTTACCTAACAAATAAGTAAAATAATTACGTCATGTATTTTGTA
1 AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
*
14327589 AATTCTACCTAACAAATAAGTAAAAT
1 AATTTTACCTAACAAATAAGTAAAAT
14327615 CATACAAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.36
Consensus pattern (47 bp):
AATTTTACCTAACAAATAAGTAAAATAATTACATCATGCATTTTATA
Found at i:14329321 original size:22 final size:21
Alignment explanation
Indices: 14329288--14329349 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
14329278 GTAAGGTGGT
*
14329288 TCCCTTAC-CCTATCAAAAGGA
1 TCCCTTGCACCTAT-AAAAGGA
**
14329309 TCTTTTGCACCTATAAAAAGGA
1 TCCCTTGCACCTAT-AAAAGGA
14329331 TCCCTTGCACCTATAAAAG
1 TCCCTTGCACCTATAAAAG
14329350 AGACTGGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 10 0.29
22 24 0.71
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (21 bp):
TCCCTTGCACCTATAAAAGGA
Found at i:14337367 original size:20 final size:20
Alignment explanation
Indices: 14337323--14337360 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14337313 AAATGGCTCA
14337323 TATCTATCAATAGATTTGGC
1 TATCTATCAATAGATTTGGC
*
14337343 TATCTATGAATAGATTTG
1 TATCTATCAATAGATTTG
14337361 CTCATCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (20 bp):
TATCTATCAATAGATTTGGC
Found at i:14338790 original size:32 final size:32
Alignment explanation
Indices: 14338727--14338791 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
14338717 TGGTATTGCT
* * * *
14338727 ATTTTTTAAATTTTTATTAATTCTTTTTAAGA
1 ATTTTCTAAAGTTTAATTAATTCTTTATAAGA
14338759 ATTTTCTAAAGTTTAATT-ATTCCTTTATAAGA
1 ATTTTCTAAAGTTTAATTAATT-CTTTATAAGA
14338791 A
1 A
14338792 ATATATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 3 0.11
32 25 0.89
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (32 bp):
ATTTTCTAAAGTTTAATTAATTCTTTATAAGA
Found at i:14340017 original size:29 final size:30
Alignment explanation
Indices: 14339972--14340028 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
14339962 TCATATATGT
*
14339972 ATATATATATATAATAAAGTAATACATATAA
1 ATATATATATATAATAAAATAA-ACATATAA
14340003 ATATATAT-TAT-ATAAAATAAACATAT
1 ATATATATATATAATAAAATAAACATAT
14340029 TAGAGATTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 6 0.24
29 8 0.32
30 3 0.12
31 8 0.32
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (30 bp):
ATATATATATATAATAAAATAAACATATAA
Found at i:14342823 original size:13 final size:14
Alignment explanation
Indices: 14342797--14342825 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
14342787 TCCGACGGTT
14342797 TTCCAACGGAAATA
1 TTCCAACGGAAATA
14342811 TTCCAAC-GAAATA
1 TTCCAACGGAAATA
14342824 TT
1 TT
14342826 TCCATTGGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (14 bp):
TTCCAACGGAAATA
Found at i:14342828 original size:14 final size:15
Alignment explanation
Indices: 14342796--14342829 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
14342786 TTCCGACGGT
14342796 TTTCCAACGGAAATA
1 TTTCCAACGGAAATA
14342811 -TTCCAAC-GAAATA
1 TTTCCAACGGAAATA
14342824 TTTCCA
1 TTTCCA
14342830 TTGGAAATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (15 bp):
TTTCCAACGGAAATA
Found at i:14343519 original size:2 final size:2
Alignment explanation
Indices: 14343512--14343545 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
14343502 TAGCTATGGA
14343512 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
14343546 CACTACAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14350399 original size:391 final size:387
Alignment explanation
Indices: 14349655--14350417 Score: 1075
Period size: 391 Copynumber: 2.0 Consensus size: 387
14349645 TTGGAACTTC
* * ** *
14349655 AACTTGGCCACTTGTTTGTGTGTGGTATATTGTGGTAATCTTATGTTTAACTCCACATTTGGCAA
1 AACTGGGCCACTTGTTTGTGGGTGGTATATCCTGGCAATCTTATGTTTAACTCCACATTTGGCAA
* * * * *
14349720 GGAATGCCTCAAACTATTTGTTGTAAAAGTGAGATCCTTTATCACTAATAATAGCTTTAGAGTGC
66 GGAATGCCTCAAACTATTTGTTGCAAAAGTAAGATCCTTCATCACTAATAATAGCTCTAGAGTAC
** * * * *
14349785 CAAAATGAGTGAAGATATTCTTTATCAAAAAGTTCAACACACTTTAGAGTCGTTATTTTAGAATG
131 CAAAACAAGTGAAGATATTCTTTATCAAAAAGTTCAACACACCTTAGAGCCATTATTCTAGAATG
*
14349850 CTACACCTTCAACCCATTTAGACACATAATCAATAGCAACTAAGATATAATGATTATGTATGAAG
196 CTACACCTTCAACCCATTTAGACACATAATCAATAACAACTAAGATATAATGATTATGTATGAAG
* ** *
14349915 GAATAAATGGACCTATGAAGTCAATTCCCTACACATAAAAAATCTTTACCTCAGGAATATTGTTG
261 GAATAAATGGACCCATGAAGTCAATTCCCTACACATAAAAAATCCATACCTCAAGAATATTGTTG
*
14349980 AAAGGCATCTCATGTCTTCTTGATATGTTGCCAACTTGCTAACATCAATTATTTGAAATTGT
326 AAAGGCATCTCATGTCTTCTTGATATGTTGCCAACTCGCTAACATCAATTATTTGAAATTGT
* * *
14350042 AACTGGGCCACTTGTTTGTGGGTGGTATGTCCTGGCAATCTTATGTTTAACTCCATATTTGGTAA
1 AACTGGGCCACTTGTTTGTGGGTGGTATATCCTGGCAATCTTATGTTTAACTCCACATTTGGCAA
* *
14350107 -GAAGTGCCTCGAAA-TATTTGTTGCAAAATTAAGATCCTTCATCATTAATAATAGCTCTAGGAG
66 GGAA-TGCCTC-AAACTATTTGTTGCAAAAGTAAGATCCTTCATCACTAATAATAGCTCTA-GAG
* *
14350170 TACCAAAAACAAGTGAAGATATTCTTTCTCAAGAAGTTCAACACCACCTTAGAGCCATTATTCTA
128 TACC-AAAACAAGTGAAGATATTCTTTATCAAAAAGTTCAACA-CACCTTAGAGCCATTATTCTA
* ** * * *
14350235 GAATGTTGTAGCTTCAACCCATTTAGACACATAATCAATAACAACTAAGATATATTGGTTATTGT
191 GAATGCTACACCTTCAACCCATTTAGACACATAATCAATAACAACTAAGATATAATGATTA-TGT
* *
14350300 ATGAATGAATAAATGGACCCATGAAGTCAATTGCCC-ACACATAAAAAATCCATACGTCAAGAAT
255 ATGAAGGAATAAATGGACCCATGAAGTCAATT-CCCTACACATAAAAAATCCATACCTCAAGAAT
* *
14350364 ATTGTTGAGAGGCATCTCTTGTC-TCTTAGATATGTTGCCAACTCGCTAACATCA
319 ATTGTTGAAAGGCATCTCATGTCTTCTT-GATATGTTGCCAACTCGCTAACATCA
14350418 TCGTACTTTT
Statistics
Matches: 329, Mismatches: 39, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
386 3 0.01
387 102 0.31
388 9 0.03
389 34 0.10
390 75 0.23
391 103 0.31
392 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (387 bp):
AACTGGGCCACTTGTTTGTGGGTGGTATATCCTGGCAATCTTATGTTTAACTCCACATTTGGCAA
GGAATGCCTCAAACTATTTGTTGCAAAAGTAAGATCCTTCATCACTAATAATAGCTCTAGAGTAC
CAAAACAAGTGAAGATATTCTTTATCAAAAAGTTCAACACACCTTAGAGCCATTATTCTAGAATG
CTACACCTTCAACCCATTTAGACACATAATCAATAACAACTAAGATATAATGATTATGTATGAAG
GAATAAATGGACCCATGAAGTCAATTCCCTACACATAAAAAATCCATACCTCAAGAATATTGTTG
AAAGGCATCTCATGTCTTCTTGATATGTTGCCAACTCGCTAACATCAATTATTTGAAATTGT
Found at i:14352153 original size:17 final size:18
Alignment explanation
Indices: 14352131--14352173 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
14352121 CAAGTGTAAG
14352131 AAAGTT-ACAGACAAACA
1 AAAGTTGACAGACAAACA
* *
14352148 AAAGTTGAGAGAGAAACA
1 AAAGTTGACAGACAAACA
14352166 AAGAGTTG
1 AA-AGTTG
14352174 TTAATTCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 11 0.50
19 5 0.23
ACGTcount: A:0.53, C:0.09, G:0.23, T:0.14
Consensus pattern (18 bp):
AAAGTTGACAGACAAACA
Found at i:14359739 original size:36 final size:36
Alignment explanation
Indices: 14359678--14359764 Score: 97
Period size: 36 Copynumber: 2.4 Consensus size: 36
14359668 ACTTCAGACA
* **
14359678 ATGATTTGATTCTTCTCCTAGTGCTTCGACACGTGC
1 ATGATTTGATTCTTCTCCCAGTGCTTCGACACGCAC
* *
14359714 GA-GATTTGATTCTT-TGCCCATTGCTTCGGCACGCAC
1 -ATGATTTGATTCTTCT-CCCAGTGCTTCGACACGCAC
14359750 ATGATTTGATTCTTC
1 ATGATTTGATTCTTC
14359765 GCCTATTACT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
35 2 0.05
36 39 0.93
37 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (36 bp):
ATGATTTGATTCTTCTCCCAGTGCTTCGACACGCAC
Done.