Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 43
Found at i:807338 original size:20 final size:20
Alignment explanation
Indices: 807313--807356 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
807303 TCCAAATTCT
*
807313 CAACGCGAATCTGTAAATTG
1 CAACGCGAATCTGTAAATAG
*
807333 CAACGCGAATTTGTAAATAG
1 CAACGCGAATCTGTAAATAG
807353 CAAC
1 CAAC
807357 ACATAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (20 bp):
CAACGCGAATCTGTAAATAG
Found at i:807375 original size:20 final size:20
Alignment explanation
Indices: 807352--807476 Score: 146
Period size: 20 Copynumber: 6.2 Consensus size: 20
807342 TTTGTAAATA
807352 GCAACACATAAGTCAAATTC
1 GCAACACATAAGTCAAATTC
* *
807372 GCAATACAGAAGTCAAATTC
1 GCAACACATAAGTCAAATTC
*
807392 GCAATACATAAGTCAAATTC
1 GCAACACATAAGTCAAATTC
* *
807412 GCAACGC-TGAATTTCAAATTC
1 GCAACACAT-AA-GTCAAATTC
*
807433 GCAACACAAAAGTCAAATTC
1 GCAACACATAAGTCAAATTC
*
807453 GCAACGCGAT-AGTCAAATTC
1 GCAACAC-ATAAGTCAAATTC
807473 GCAA
1 GCAA
807477 AGCGCGTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.01
20 72 0.80
21 17 0.19
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (20 bp):
GCAACACATAAGTCAAATTC
Found at i:807401 original size:40 final size:39
Alignment explanation
Indices: 807352--807476 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 39
807342 TTTGTAAATA
**
807352 GCAACACATAAGTCAAATTCGCAATACAGAAGTCAAATTC
1 GCAACACATAAGTCAAATTCGCAACGC-GAAGTCAAATTC
* *
807392 GCAATACATAAGTCAAATTCGCAACGCTGAATTTCAAATTC
1 GCAACACATAAGTCAAATTCGCAACGC-GAA-GTCAAATTC
*
807433 GCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTC
1 GCAACACATAAGTCAAATTCGCAACGCGA-AGTCAAATTC
807473 GCAA
1 GCAA
807477 AGCGCGTTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 41 0.55
41 34 0.45
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (39 bp):
GCAACACATAAGTCAAATTCGCAACGCGAAGTCAAATTC
Found at i:807448 original size:81 final size:79
Alignment explanation
Indices: 807327--807476 Score: 205
Period size: 81 Copynumber: 1.9 Consensus size: 79
807317 GCGAATCTGT
* * *
807327 AAATTGCAACGCGAATTTGTAAATAGCAACACATAAGTCAAATTCGCAATACAGA-AGTCAAATT
1 AAATTGCAACGCGAATTTGCAAATAGCAACACAAAAGTCAAATTCGCAACAC-GATAGTCAAATT
807391 CGCAATACATAAGTC
65 CGCAATACATAAGTC
* *
807406 AAATTCGCAACGCTGAATTT-CAAATTCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAA
1 AAATT-GCAACGC-GAATTTGCAAA-TAGCAACACAAAAGTCAAATTCGCAACACGATAGTCAAA
807470 TTCGCAA
63 TTCGCAA
807477 AGCGCGTTTA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
79 5 0.08
80 12 0.19
81 45 0.73
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (79 bp):
AAATTGCAACGCGAATTTGCAAATAGCAACACAAAAGTCAAATTCGCAACACGATAGTCAAATTC
GCAATACATAAGTC
Found at i:808067 original size:20 final size:20
Alignment explanation
Indices: 808024--808067 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
808014 GCAACGCGAT
* * * *
808024 TTTCTCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
808044 TTTCGCGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
808064 TTTC
1 TTTC
808068 AGAAACTACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:810244 original size:21 final size:21
Alignment explanation
Indices: 810205--810244 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
810195 TGCACTTATC
* *
810205 ATCGTTCAAGAGGCGCCTCCT
1 ATCGTTCAAGAGACCCCTCCT
810226 ATCGTTCAAGAGACCCCTC
1 ATCGTTCAAGAGACCCCTC
810245 TCATCATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGTTCAAGAGACCCCTCCT
Found at i:810278 original size:21 final size:21
Alignment explanation
Indices: 810254--810301 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
810244 CTCATCATCG
*
810254 AAGAGGCCCCTCTTACCGTTT
1 AAGAGGCCCCTCTCACCGTTT
* *
810275 AAGAGGCCCCTGTCATCGTTT
1 AAGAGGCCCCTCTCACCGTTT
810296 AAGAGG
1 AAGAGG
810302 TCCCGCCTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (21 bp):
AAGAGGCCCCTCTCACCGTTT
Found at i:810300 original size:42 final size:42
Alignment explanation
Indices: 810203--810321 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
810193 GATGCACTTA
* *
810203 TCATCGTTCAAGAGGCGCCTCCTATCGTTCAAGAGACCCCTC
1 TCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAGACCCCTC
* * * * *
810245 TCATC-ATCGAAGAGGCCCCTCTTACCGTTTAAGAGGCCCCTG
1 TCATCGTTC-AAGAGGCCCCTCCTACCGTTCAAGAGACCCCTC
* * * * *
810287 TCATCGTTTAAGAGGTCCCGCCTGCAGTTCAAGAG
1 TCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAG
810322 CCCGATTTAC
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 2 0.03
42 57 0.95
43 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCTACCGTTCAAGAGACCCCTC
Found at i:811943 original size:34 final size:34
Alignment explanation
Indices: 811892--811972 Score: 119
Period size: 34 Copynumber: 2.4 Consensus size: 34
811882 GCAACGTGAA
* * *
811892 AGTCAAATTCGCGTTGCGATTTTC-TCGTTGCGAT
1 AGTCAAATTTGCATTGCGATTTTCGT-GTTGCAAT
811926 AGTCAAATTTGCATTGCGATTTTCGTGTTGCAAT
1 AGTCAAATTTGCATTGCGATTTTCGTGTTGCAAT
811960 AGTCAAATTTGCA
1 AGTCAAATTTGCA
811973 ACGTTAAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
34 42 0.98
35 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.38
Consensus pattern (34 bp):
AGTCAAATTTGCATTGCGATTTTCGTGTTGCAAT
Found at i:811993 original size:20 final size:20
Alignment explanation
Indices: 811955--812011 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
811945 TTTTCGTGTT
* *
811955 GCAATAGTCAAATTTGCAAC
1 GCAAAAGTCAAATTCGCAAC
** *
811975 GTTAAAGTTAAATTCGCAAC
1 GCAAAAGTCAAATTCGCAAC
811995 GCAAAAGTCAAATTCGC
1 GCAAAAGTCAAATTCGC
812012 GTTGTGATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (20 bp):
GCAAAAGTCAAATTCGCAAC
Found at i:812311 original size:18 final size:18
Alignment explanation
Indices: 812288--812323 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
812278 AAGTCGGTTG
*
812288 TGATTGGGATTTTGATTT
1 TGATTGAGATTTTGATTT
812306 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
812324 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:814605 original size:24 final size:24
Alignment explanation
Indices: 814571--814624 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
814561 CTGAAACATC
814571 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
814595 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
814619 ATCAAA
1 ATCAAA
814625 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:814638 original size:24 final size:24
Alignment explanation
Indices: 814571--814638 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
814561 CTGAAACATC
* * *
814571 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
814595 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
814619 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
814639 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:814789 original size:22 final size:22
Alignment explanation
Indices: 814761--814814 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
814751 GTATTGGAAA
814761 TGTGGTGAAACAAAATTTTCTT
1 TGTGGTGAAACAAAATTTTCTT
814783 TGTGGTGAAACAAAATTTTCTT
1 TGTGGTGAAACAAAATTTTCTT
*
814805 TGTGATGAAA
1 TGTGGTGAAA
814815 TTGTAGTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.39
Consensus pattern (22 bp):
TGTGGTGAAACAAAATTTTCTT
Found at i:815634 original size:20 final size:21
Alignment explanation
Indices: 815585--815634 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
815575 TTAAATTCGT
815585 GTTGCGAA-TTCGAAAATCGA
1 GTTGCGAATTTCGAAAATCGA
* * *
815605 GTTGTG-ATTTTGAAATTC-A
1 GTTGCGAATTTCGAAAATCGA
815624 GTTGCGAATTT
1 GTTGCGAATTT
815635 GACTTATGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (21 bp):
GTTGCGAATTTCGAAAATCGA
Found at i:815635 original size:19 final size:20
Alignment explanation
Indices: 815566--815636 Score: 74
Period size: 19 Copynumber: 3.6 Consensus size: 20
815556 AATAAAACCT
* *
815566 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* *
815585 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGA
* *
815605 GTTGTGATTTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
815624 GTTGCGAATTTGA
1 GTTGCGAATTTGA
815637 CTTATGTGTT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 21 0.51
20 20 0.49
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:815647 original size:20 final size:20
Alignment explanation
Indices: 815624--815710 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
815614 TTGAAATTCA
*
815624 GTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTTTTGT
*
815644 GTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
815664 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTTGT
*
815684 GTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTTTTGT
815704 GTTGCGA
1 GTTGCGA
815711 TTTACAAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.17, C:0.11, G:0.25, T:0.46
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTTGT
Found at i:815727 original size:20 final size:20
Alignment explanation
Indices: 815704--815743 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
815694 TGACTTCTGT
815704 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
815724 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
815744 AACGCGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:815728 original size:40 final size:40
Alignment explanation
Indices: 815624--815730 Score: 103
Period size: 40 Copynumber: 2.7 Consensus size: 40
815614 TTGAAATTCA
* * * *
815624 GTTGCGAATTTGAC-TTATGTGTTGCAAATTTGACTTTTGT
1 GTTGCGAATTTGACATT-CGCGTTGCGAATTTGACTTCTGT
* * *
815664 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACATTCGCGTTGCGAATTTGACTTCTGT
815704 GTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 GTTGCGAATTTGAC--ATTCGCGTTGCGA
815731 TTTACATATT
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
38 2 0.03
39 4 0.07
40 51 0.86
41 2 0.03
ACGTcount: A:0.19, C:0.13, G:0.24, T:0.44
Consensus pattern (40 bp):
GTTGCGAATTTGACATTCGCGTTGCGAATTTGACTTCTGT
Found at i:815750 original size:20 final size:20
Alignment explanation
Indices: 815707--815750 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
815697 CTTCTGTGTT
***
815707 GCGATTTACAAATTCGCGTT
1 GCGATTTACAAATTCGCAAC
*
815727 GCGATTTACATATTCGCAAC
1 GCGATTTACAAATTCGCAAC
815747 GCGA
1 GCGA
815751 ATTTGGAAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
GCGATTTACAAATTCGCAAC
Found at i:821118 original size:21 final size:21
Alignment explanation
Indices: 821092--821133 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
821082 TGTCGATATG
821092 GCTGTAACTTCAGGTACACTT
1 GCTGTAACTTCAGGTACACTT
821113 GCTGTAACTTCAGGTACACTT
1 GCTGTAACTTCAGGTACACTT
821134 CTTCCCCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (21 bp):
GCTGTAACTTCAGGTACACTT
Found at i:829378 original size:8 final size:8
Alignment explanation
Indices: 829365--829406 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
829355 GATAGAATAA
829365 AATAAAAT
1 AATAAAAT
*
829373 AATAAAAG
1 AATAAAAT
*
829381 GA-AAAAT
1 AATAAAAT
829388 AATAAAAT
1 AATAAAAT
829396 AATAAAAT
1 AATAAAAT
829404 AAT
1 AAT
829407 GATTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 5 0.17
8 24 0.83
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (8 bp):
AATAAAAT
Found at i:829970 original size:11 final size:12
Alignment explanation
Indices: 829956--829985 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
829946 TGAAAAGTAT
829956 GAGAAAA-TAGA
1 GAGAAAACTAGA
829967 GAGAAAACTAGA
1 GAGAAAACTAGA
829979 GAGAAAA
1 GAGAAAA
829986 AGAAGATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.03, G:0.27, T:0.07
Consensus pattern (12 bp):
GAGAAAACTAGA
Found at i:830147 original size:12 final size:12
Alignment explanation
Indices: 830130--830157 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
830120 AATACCTAAA
830130 AAATAATATTCT
1 AAATAATATTCT
830142 AAATAATATTCT
1 AAATAATATTCT
830154 AAAT
1 AAAT
830158 CCTAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (12 bp):
AAATAATATTCT
Found at i:830176 original size:72 final size:76
Alignment explanation
Indices: 830079--830274 Score: 226
Period size: 77 Copynumber: 2.6 Consensus size: 76
830069 AAGCTAAAAC
*
830079 ATCTTAAATCATAA-TAAAACACTAAAAACTATTTAAACTAAAATACCT-AAA-A-A-ATAATAT
1 ATCTTAAATCATAATTAAAACACTAAAAACTATTTAAACTAAAATACCTAAAACACAGATAAAAT
**
830139 -TCTAAATAAT
66 ATAAAAATAAT
* * *
830149 AT-TCTAAATCCTAATTAAAAGGACTAAAACCTATTTAAACTAAAATACCTAAAACACAGATAAA
1 ATCT-TAAATCATAATTAAAA-CACTAAAAACTATTTAAACTAAAATACCTAAAACACAGATAAA
830213 ATATAAAAATAAT
64 ATATAAAAATAAT
* * *
830226 ATCTTAAAACTTAATTAAAATACTAAAAAACATATTTAAACTAAAATAC
1 ATCTTAAATCATAATTAAAACACT-AAAAAC-TATTTAAACTAAAATAC
830275 AAAGATAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
69 1 0.01
70 11 0.10
71 5 0.05
72 27 0.26
73 3 0.03
74 1 0.01
75 1 0.01
76 9 0.09
77 29 0.28
78 18 0.17
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.29
Consensus pattern (76 bp):
ATCTTAAATCATAATTAAAACACTAAAAACTATTTAAACTAAAATACCTAAAACACAGATAAAAT
ATAAAAATAAT
Found at i:830899 original size:23 final size:23
Alignment explanation
Indices: 830869--830916 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
830859 GGCCGGGTAT
830869 ATATATATATATATTTAAATTAA
1 ATATATATATATATTTAAATTAA
* *
830892 ATATATATTTTTATTTAAATTAA
1 ATATATATATATATTTAAATTAA
830915 AT
1 AT
830917 TTATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATATATATATTTAAATTAA
Found at i:831017 original size:13 final size:13
Alignment explanation
Indices: 830961--831004 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
830951 TTTAATATTT
*
830961 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
830973 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
*
830986 ATCGGGGCAGGTA
1 ATCGGGGCGGGTA
830999 ATCGGG
1 ATCGGG
831005 TAATCGAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:835478 original size:8 final size:8
Alignment explanation
Indices: 835465--835513 Score: 68
Period size: 8 Copynumber: 6.4 Consensus size: 8
835455 GATAGAATAA
835465 AATAAAAT
1 AATAAAAT
835473 AATAAAA-
1 AATAAAAT
835480 AGA-AAAAT
1 A-ATAAAAT
835488 AATAAAAT
1 AATAAAAT
835496 AATAAAAT
1 AATAAAAT
835504 AAT-AAAT
1 AATAAAAT
835511 AAT
1 AAT
835514 GATTTTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
7 13 0.34
8 25 0.66
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (8 bp):
AATAAAAT
Found at i:835510 original size:15 final size:15
Alignment explanation
Indices: 835465--835513 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
835455 GATAGAATAA
835465 AATAAAATAATAAA-
1 AATAAAATAATAAAT
*
835479 AAGAAAAATAATAAAAT
1 AA-TAAAATAAT-AAAT
835496 AATAAAATAATAAAT
1 AATAAAATAATAAAT
835511 AAT
1 AAT
835514 GATTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 2 0.07
15 15 0.50
16 11 0.37
17 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:835606 original size:17 final size:17
Alignment explanation
Indices: 835581--835614 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
835571 ATGAGATAAA
*
835581 AAATTAAATAAACAAAT
1 AAATAAAATAAACAAAT
*
835598 AAATAAAATAAATAAAT
1 AAATAAAATAAACAAAT
835615 TGAGAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAACAAAT
Found at i:837013 original size:12 final size:12
Alignment explanation
Indices: 836996--837021 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
836986 ATATTGTTTT
836996 ATTTTTTAAATA
1 ATTTTTTAAATA
837008 ATTTTTTAAATA
1 ATTTTTTAAATA
837020 AT
1 AT
837022 CTAAGGTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTTTTAAATA
Found at i:837280 original size:28 final size:27
Alignment explanation
Indices: 837228--837282 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
837218 CCTCTAACTT
837228 AAAACCCTAAATTATAAACCCTAAACC
1 AAAACCCTAAATTATAAACCCTAAACC
* * *
837255 AAAACCCATAACTTTTAAGCCCTAAACC
1 AAAACCC-TAAATTATAAACCCTAAACC
837283 CTAACTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.47, C:0.31, G:0.02, T:0.20
Consensus pattern (27 bp):
AAAACCCTAAATTATAAACCCTAAACC
Found at i:840860 original size:13 final size:13
Alignment explanation
Indices: 840831--840859 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
840821 GTCAATTCTC
840831 TTTTCTCTTTATT
1 TTTTCTCTTTATT
840844 TTTTCT-TTTATT
1 TTTTCTCTTTATT
840856 TTTT
1 TTTT
840860 TAATAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTCTCTTTATT
Found at i:841512 original size:4 final size:4
Alignment explanation
Indices: 841503--841533 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
841493 CAATGCATGT
841503 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
841534 CATAGTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:841832 original size:29 final size:29
Alignment explanation
Indices: 841790--841846 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
841780 CAGTGGCAAC
841790 ATAGGTCGCCATGCACGCCCGGCGTCCTT
1 ATAGGTCGCCATGCACGCCCGGCGTCCTT
841819 ATAGGTCGCCATGCACGCCCGGCGTCCT
1 ATAGGTCGCCATGCACGCCCGGCGTCCT
841847 ATAATTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.39, G:0.28, T:0.19
Consensus pattern (29 bp):
ATAGGTCGCCATGCACGCCCGGCGTCCTT
Found at i:841881 original size:13 final size:13
Alignment explanation
Indices: 841863--841919 Score: 78
Period size: 13 Copynumber: 4.1 Consensus size: 13
841853 ATTTGCTTGG
841863 GGTGGCCGCTGTT
1 GGTGGCCGCTGTT
841876 GGTGGCCGCTGCTTT
1 GGTGGCCGCTG--TT
841891 GGGGTGGCCGCTGTT
1 --GGTGGCCGCTGTT
841906 GGTGGCCGCTGTT
1 GGTGGCCGCTGTT
841919 G
1 G
841920 CTCGTCCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 25 0.62
15 4 0.10
17 11 0.28
ACGTcount: A:0.00, C:0.23, G:0.47, T:0.30
Consensus pattern (13 bp):
GGTGGCCGCTGTT
Found at i:841893 original size:30 final size:30
Alignment explanation
Indices: 841859--841916 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
841849 AATTATTTGC
841859 TTGGGGTGGCCGCTGTTGGTGGCCGCTGCT
1 TTGGGGTGGCCGCTGTTGGTGGCCGCTGCT
841889 TTGGGGTGGCCGCTGTTGGTGGCCGCTG
1 TTGGGGTGGCCGCTGTTGGTGGCCGCTG
841917 TTGCTCGTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.00, C:0.22, G:0.48, T:0.29
Consensus pattern (30 bp):
TTGGGGTGGCCGCTGTTGGTGGCCGCTGCT
Found at i:842202 original size:12 final size:12
Alignment explanation
Indices: 842185--842209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
842175 CCGACGACAT
842185 GGTAGGTGGTAG
1 GGTAGGTGGTAG
842197 GGTAGGTGGTAG
1 GGTAGGTGGTAG
842209 G
1 G
842210 TCGCCATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.60, T:0.24
Consensus pattern (12 bp):
GGTAGGTGGTAG
Found at i:842285 original size:35 final size:35
Alignment explanation
Indices: 842246--842313 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
842236 TCCTGCATCG
* *
842246 CGACCCAGTTTTAACTGTAGCACTCATGCATGCAA
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
*
842281 CGACCAAGCTTTAACTGTATCACTCATGCATGC
1 CGACCAAGCTTTAACTGTAGCACTCATGCATGC
842314 GTTGCATCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (35 bp):
CGACCAAGCTTTAACTGTAGCACTCATGCATGCAA
Found at i:842772 original size:21 final size:21
Alignment explanation
Indices: 842747--842790 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
842737 AATCTAGTTA
*
842747 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTGGTTAGTATAAATT
* *
842768 ATTAGTTGGTTAGTTTAAGTT
1 ATTAGTTGGTTAGTATAAATT
842789 AT
1 AT
842791 ATATTATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (21 bp):
ATTAGTTGGTTAGTATAAATT
Found at i:843309 original size:18 final size:20
Alignment explanation
Indices: 843285--843333 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 20
843275 GAGATAATTT
*
843285 TTGTTTAAAAAT-TATATTG
1 TTGTTTAAAAATATATAGTG
*
843304 -TGTTTAAAAATATTTAGTG
1 TTGTTTAAAAATATATAGTG
843323 TTGTTTAAAAA
1 TTGTTTAAAAA
843334 AAAATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 5 0.19
20 10 0.38
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (20 bp):
TTGTTTAAAAATATATAGTG
Found at i:843587 original size:26 final size:25
Alignment explanation
Indices: 843558--843622 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 25
843548 AAATCATATT
*
843558 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AATAAATATCAAATC
* *
843584 ATTAGATT-AATAATAATTATTAAATC
1 ATT--ATTAAATAATAAATATCAAATC
843610 ATTATT-AATAATA
1 ATTATTAAATAATA
843623 TTAGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 10 0.29
26 18 0.53
27 3 0.09
28 3 0.09
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ATTATTAAATAATAAATATCAAATC
Found at i:846539 original size:26 final size:26
Alignment explanation
Indices: 846513--846864 Score: 265
Period size: 26 Copynumber: 14.2 Consensus size: 26
846503 GATGATTTAG
*
846513 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
846539 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
846565 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
846591 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
846614 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
846637 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
846663 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
846689 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
846715 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
846738 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
846761 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
* * *
846787 TAATGATTTTATAATAATTATTAT-G
1 TAATGATTTGATAATAATCATTATAA
* * *
846812 TTATTATTT-AGTAATTAT--TTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
846836 TAATGATTTAATACTAATGATT-TAA
1 TAATGATTTGATAATAATCATTATAA
846861 TAAT
1 TAAT
846865 TATTACTAAT
Statistics
Matches: 261, Mismatches: 44, Indels: 43
0.75 0.13 0.12
Matches are distributed among these distances:
21 8 0.03
22 6 0.02
23 28 0.11
24 27 0.10
25 35 0.13
26 155 0.59
27 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:846675 original size:124 final size:124
Alignment explanation
Indices: 846455--846848 Score: 695
Period size: 124 Copynumber: 3.2 Consensus size: 124
846445 ATGTATTTAT
846455 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
846520 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
846579 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
846644 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
846703 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
846768 TTGATAATAATCATTATAATAATGATTTTATAATAATTATTAT-GTTATTATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* *
846826 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
846849 CTAATGATTT
Statistics
Matches: 262, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
121 18 0.07
123 15 0.06
124 229 0.87
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:846855 original size:14 final size:14
Alignment explanation
Indices: 846823--846864 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
846813 TATTATTTAG
*
846823 TAATTATTT-ATAA
1 TAATGATTTAATAA
*
846836 TAATGATTTAATAC
1 TAATGATTTAATAA
846850 TAATGATTTAATAA
1 TAATGATTTAATAA
846864 T
1 T
846865 TATTACTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 8 0.32
14 17 0.68
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:846887 original size:38 final size:38
Alignment explanation
Indices: 846817--846890 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
846807 TTATGTTATT
* **
846817 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
846855 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
846891 CAAAGTAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:846985 original size:14 final size:14
Alignment explanation
Indices: 846966--847048 Score: 63
Period size: 14 Copynumber: 6.2 Consensus size: 14
846956 TTTAAATATT
846966 TAATGATTTGATAC
1 TAATGATTTGATAC
846980 TAATGA-TT--TAC
1 TAATGATTTGATAC
*
846991 TAAT--TAT--TAC
1 TAATGATTTGATAC
*
847001 TAATGATTTAATAC
1 TAATGATTTGATAC
*
847015 TAATTATTTGATAC
1 TAATGATTTGATAC
847029 TAGTAATGATTTGATAC
1 ---TAATGATTTGATAC
847046 TAA
1 TAA
847049 ACATCATTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
10 8 0.14
11 7 0.12
12 2 0.04
13 2 0.04
14 24 0.43
17 13 0.23
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.45
Consensus pattern (14 bp):
TAATGATTTGATAC
Found at i:847002 original size:10 final size:11
Alignment explanation
Indices: 846977--847010 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
846967 AATGATTTGA
846977 TACTAATGATT
1 TACTAATGATT
*
846988 TACTAATTA-T
1 TACTAATGATT
846998 TACTAATGATT
1 TACTAATGATT
847009 TA
1 TA
847011 ATACTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TACTAATGATT
Found at i:847020 original size:21 final size:21
Alignment explanation
Indices: 846977--847020 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
846967 AATGATTTGA
* *
846977 TACTAATGATTTACTAATTAT
1 TACTAATGATTTAATAATAAT
*
846998 TACTAATGATTTAATACTAAT
1 TACTAATGATTTAATAATAAT
847019 TA
1 TA
847021 TTTGATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TACTAATGATTTAATAATAAT
Found at i:847040 original size:17 final size:17
Alignment explanation
Indices: 847015--847047 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
847005 GATTTAATAC
*
847015 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
847032 TAATGATTTGATACTA
1 TAATGATTTGATACTA
847048 AACATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:847984 original size:23 final size:21
Alignment explanation
Indices: 847958--848010 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
847948 TTACAAAAAC
*
847958 AATAAAATTTATTTAAATTAGAT
1 AATAAAATTAATTTAAA-TA-AT
* *
847981 AATATAGTTAATTTAAATAAT
1 AATAAAATTAATTTAAATAAT
848002 AATTAAAAT
1 AA-TAAAAT
848011 ATACAAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 4 0.17
22 6 0.25
23 14 0.58
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (21 bp):
AATAAAATTAATTTAAATAAT
Found at i:849214 original size:15 final size:15
Alignment explanation
Indices: 849191--849228 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
849181 TACAACACTA
849191 AACTT-TAATATAAT
1 AACTTATAATATAAT
849205 AACTTATAATATAAT
1 AACTTATAATATAAT
*
849220 AACTAATAA
1 AACTTATAA
849229 ACTAACAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (15 bp):
AACTTATAATATAAT
Found at i:849356 original size:30 final size:34
Alignment explanation
Indices: 849282--849361 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 34
849272 CCAAACCCTT
* *
849282 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
849315 AAACTAACTAATAAACTATTTTTTCAT-T-A-TA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
*
849346 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
849362 TACTAACTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 11 0.26
31 6 0.14
32 1 0.02
33 5 0.12
34 20 0.47
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:849500 original size:46 final size:48
Alignment explanation
Indices: 849402--849505 Score: 126
Period size: 46 Copynumber: 2.2 Consensus size: 48
849392 CAACAAACAA
**
849402 ATATAACTTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAACAAAAACTAATTAAATAATTTTTACT
*
849451 ATATAACTAACTA-TTAAC-AA-AACAAACTAATT-AATTATTTTTAACT
1 ATATAACTAACTATTTAACTAACAA-AAACTAATTAAATAATTTTT-ACT
849497 ATATAACTA
1 ATATAACTA
849506 TCAAACATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
45 11 0.22
46 21 0.42
47 5 0.10
48 6 0.12
49 7 0.14
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAACAAAAACTAATTAAATAATTTTTACT
Found at i:849625 original size:16 final size:18
Alignment explanation
Indices: 849596--849634 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
849586 ACTAATTAAC
*
849596 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
849614 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
849630 ATTTA
1 ATTTA
849635 CCTTATATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:849966 original size:50 final size:50
Alignment explanation
Indices: 849849--849956 Score: 186
Period size: 50 Copynumber: 2.2 Consensus size: 50
849839 TAGGATCACA
*
849849 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
849898 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTAT-T
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
849947 TGGC-TGCATG
1 TGGCATGCATG
849957 TGCATGCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
48 6 0.11
49 13 0.23
50 38 0.67
ACGTcount: A:0.22, C:0.19, G:0.39, T:0.20
Consensus pattern (50 bp):
TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTATCT
Found at i:850026 original size:29 final size:29
Alignment explanation
Indices: 849994--850085 Score: 148
Period size: 29 Copynumber: 3.2 Consensus size: 29
849984 ACGCCGGGGT
849994 GACCTACAAGGTCGCCGGGACTACATGGC
1 GACCTACAAGGTCGCCGGGACTACATGGC
850023 GACCTACAAGGTCGCCGGGACTACATGGC
1 GACCTACAAGGTCGCCGGGACTACATGGC
* ** *
850052 GACCTATAAGGTCGCCCAGACTGCATGGC
1 GACCTACAAGGTCGCCGGGACTACATGGC
850081 GACCT
1 GACCT
850086 CTCTATTGGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.24, C:0.32, G:0.29, T:0.15
Consensus pattern (29 bp):
GACCTACAAGGTCGCCGGGACTACATGGC
Found at i:850114 original size:32 final size:32
Alignment explanation
Indices: 850072--850143 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
850062 GTCGCCCAGA
*
850072 CTGCATGGCGACCTCTCTATTGGCTGGCTCCT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCCT
* * *
850104 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCCT
850136 CTGCATGG
1 CTGCATGG
850144 TGAGTATATG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.08, C:0.32, G:0.29, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCCT
Found at i:850183 original size:39 final size:33
Alignment explanation
Indices: 850128--850240 Score: 172
Period size: 33 Copynumber: 3.2 Consensus size: 33
850118 CTCCGTTGGC
850128 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
1 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
850161 TGGCTCGTCTGCATGGTGATGGTGAGTATATGGCTTGTA
1 TGGCTCGTCTGC------ATGGTGAGTATATGGCTTGTA
850200 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
1 TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
850233 TGGCTCGT
1 TGGCTCGT
850241 ATGTCACTCG
Statistics
Matches: 74, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
33 41 0.55
39 33 0.45
ACGTcount: A:0.14, C:0.15, G:0.35, T:0.36
Consensus pattern (33 bp):
TGGCTCGTCTGCATGGTGAGTATATGGCTTGTA
Found at i:856139 original size:23 final size:23
Alignment explanation
Indices: 856095--856140 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
856085 TTTATCTCCT
* *
856095 AAAATTTTATAATTCATTTTTAA
1 AAAATTATATAATTCATCTTTAA
856118 AAAATTATA-AATTCACTCTTTAA
1 AAAATTATATAATTCA-TCTTTAA
856141 TATAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAATTATATAATTCATCTTTAA
Found at i:857998 original size:14 final size:14
Alignment explanation
Indices: 857979--858007 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
857969 CGCCACTTCT
857979 GTTAAAAATTAACG
1 GTTAAAAATTAACG
857993 GTTAAAAATTAACG
1 GTTAAAAATTAACG
858007 G
1 G
858008 CCAGTGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (14 bp):
GTTAAAAATTAACG
Found at i:859474 original size:39 final size:39
Alignment explanation
Indices: 859431--859598 Score: 167
Period size: 39 Copynumber: 4.3 Consensus size: 39
859421 AGGACCTGCA
* *
859431 GTAAGGATTTACCCTGTGCACAAAGCCGATAAGCATGCG
1 GTAAGGACTTACCCTGAGCACAAAGCCGATAAGCATGCG
* * * * *
859470 GTAAGGACTTACCTTGAGCACAAAGTCGCTGAGCTTGCG
1 GTAAGGACTTACCCTGAGCACAAAGCCGATAAGCATGCG
* * * * *
859509 GTAAGGACTTACCCTAAGCACAAAGACGAGATGCCTGCG
1 GTAAGGACTTACCCTGAGCACAAAGCCGATAAGCATGCG
* * * *
859548 ATAAGGACTTACCCTGAACACAAAGCTGATGAA-CGTGCG
1 GTAAGGACTTACCCTGAGCACAAAGCCGAT-AAGCATGCG
*
859587 GTAAGGTCTTAC
1 GTAAGGACTTAC
859599 AAGTCATAGA
Statistics
Matches: 103, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
39 102 0.99
40 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (39 bp):
GTAAGGACTTACCCTGAGCACAAAGCCGATAAGCATGCG
Found at i:859560 original size:78 final size:78
Alignment explanation
Indices: 859431--859598 Score: 194
Period size: 78 Copynumber: 2.2 Consensus size: 78
859421 AGGACCTGCA
* ** * * * * *
859431 GTAAGGATTTACCCTGTGCACAAAGCCGATAAGCATGCGGTAAGGACTTACCTTGAGCACAAAG-
1 GTAAGGACTTACCCTAAGCACAAAGACGAGAAGCATGCGATAAGGACTTACCCTGAACACAAAGC
* * *
859495 TCGCTGAGCTTGCG
66 T-GATGAACGTGCG
* *
859509 GTAAGGACTTACCCTAAGCACAAAGACGAGATGCCTGCGATAAGGACTTACCCTGAACACAAAGC
1 GTAAGGACTTACCCTAAGCACAAAGACGAGAAGCATGCGATAAGGACTTACCCTGAACACAAAGC
859574 TGATGAACGTGCG
66 TGATGAACGTGCG
*
859587 GTAAGGTCTTAC
1 GTAAGGACTTAC
859599 AAGTCATAGA
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
78 74 0.99
79 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (78 bp):
GTAAGGACTTACCCTAAGCACAAAGACGAGAAGCATGCGATAAGGACTTACCCTGAACACAAAGC
TGATGAACGTGCG
Found at i:860362 original size:7 final size:7
Alignment explanation
Indices: 860350--860379 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
860340 GTCAATGTTT
860350 GTCAACG
1 GTCAACG
860357 GTCAACG
1 GTCAACG
860364 GTCAA-G
1 GTCAACG
860370 GTCAACG
1 GTCAACG
860377 GTC
1 GTC
860380 GTTAATGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:860374 original size:13 final size:14
Alignment explanation
Indices: 860350--860379 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
860340 GTCAATGTTT
860350 GTCAACGGTCAACG
1 GTCAACGGTCAACG
860364 GTCAA-GGTCAACG
1 GTCAACGGTCAACG
860377 GTC
1 GTC
860380 GTTAATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:865460 original size:25 final size:25
Alignment explanation
Indices: 865426--865473 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
865416 ATAATTAGCA
865426 AAAAAAATAATTAATTA-ATAAATTT
1 AAAAAAATAA-TAATTATATAAATTT
865451 AAAAAAATAATAATTATATAAAT
1 AAAAAAATAATAATTATATAAAT
865474 ATTATTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAAAAATAATAATTATATAAATTT
Found at i:865489 original size:33 final size:31
Alignment explanation
Indices: 865452--865528 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 31
865442 AATAAATTTA
*
865452 AAAAAATAATAATTATATAAATATTATTTTAAT
1 AAAAAATAATAATT-TATAAA-ATTATATTAAT
* *
865485 AAAAACTAAT-ATTTATATAATTATATTAAT
1 AAAAAATAATAATTTATAAAATTATATTAAT
865515 ATAAAATATAATAA
1 A-AAAA-ATAATAA
865529 CTATTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
30 11 0.30
31 9 0.24
32 7 0.19
33 10 0.27
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
AAAAAATAATAATTTATAAAATTATATTAAT
Found at i:865504 original size:18 final size:17
Alignment explanation
Indices: 865442--865504 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
865432 ATAATTAATT
865442 AATAA-ATTTA-A-AAA
1 AATAATATTTATATAAA
*
865456 AATAATAATTATATAAA
1 AATAATATTTATATAAA
* *
865473 TATTAT-TTTA-ATAAA
1 AATAATATTTATATAAA
865488 AACTAATATTTATATAA
1 AA-TAATATTTATATAA
865505 TTATATTAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
14 5 0.14
15 10 0.27
16 7 0.19
17 11 0.30
18 4 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATATTTATATAAA
Found at i:865519 original size:32 final size:33
Alignment explanation
Indices: 865452--865528 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
865442 AATAAATTTA
*
865452 AAAAAATAATAATTATATAAATATTATTTTAAT
1 AAAAAATAATAATTATATAAATATTATTATAAT
* * *
865485 AAAAACTAATATTTATATAATTA-TATTA-ATAT
1 AAAAAATAATAATTATATAAATATTATTATA-AT
*
865517 AAAATATAATAA
1 AAAAAATAATAA
865529 CTATTTTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
31 1 0.03
32 15 0.42
33 20 0.56
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (33 bp):
AAAAAATAATAATTATATAAATATTATTATAAT
Found at i:865537 original size:24 final size:22
Alignment explanation
Indices: 865501--865545 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
865491 TAATATTTAT
*
865501 ATAATTATATTAATATAAAATATA
1 ATAACTATATTAA-A-AAAATATA
*
865525 ATAACTATTTTAAAAAAATAT
1 ATAACTATATTAAAAAAATAT
865546 TAACTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAACTATATTAAAAAAATATA
Found at i:868774 original size:3 final size:3
Alignment explanation
Indices: 868766--868800 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
868756 TAAGTACTAG
868766 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
868801 ACAAAAAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:873306 original size:17 final size:18
Alignment explanation
Indices: 873269--873309 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
873259 ATATTATGTA
*
873269 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
873287 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
873304 TTTACT
1 TTTACT
873310 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:875216 original size:9 final size:9
Alignment explanation
Indices: 875204--875241 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
875194 ACCTGCTAAG
875204 GACGACGAT
1 GACGACGAT
*
875213 GACGACGAC
1 GACGACGAT
875222 GACGACGAT
1 GACGACGAT
875231 GACGACGAT
1 GACGACGAT
875240 GA
1 GA
875242 TGACAGCGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.34, C:0.24, G:0.34, T:0.08
Consensus pattern (9 bp):
GACGACGAT
Found at i:875219 original size:3 final size:3
Alignment explanation
Indices: 875204--875238 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
875194 ACCTGCTAAG
* *
875204 GAC GAC GAT GAC GAC GAC GAC GAC GAT GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
875239 TGATGACAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.26, G:0.34, T:0.06
Consensus pattern (3 bp):
GAC
Found at i:875219 original size:12 final size:12
Alignment explanation
Indices: 875207--875245 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
875197 TGCTAAGGAC
* *
875207 GACGATGACGAC
1 GACGACGACGAT
875219 GACGACGACGAT
1 GACGACGACGAT
*
875231 GACGACGATGAT
1 GACGACGACGAT
875243 GAC
1 GAC
875246 AGCGAGGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.33, C:0.23, G:0.33, T:0.10
Consensus pattern (12 bp):
GACGACGACGAT
Found at i:875498 original size:35 final size:33
Alignment explanation
Indices: 875459--875543 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
875449 ATATTTCAGT
875459 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
875494 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
875529 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
875544 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:879199 original size:41 final size:41
Alignment explanation
Indices: 879120--879201 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
879110 AATTCACCCA
* * * *
879120 CCCTACGTGGCGTATAGCGCTGCCCATGGTCCGCGCTATAC
1 CCCTACGTGGCGTATAGCGCGGACCAGGGGCCGCGCTATAC
* * *
879161 CCCTACGTGGCGTATAGCGCGGATCAGGGGGCGTGCTATAC
1 CCCTACGTGGCGTATAGCGCGGACCAGGGGCCGCGCTATAC
879202 ACACGTGTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.21
Consensus pattern (41 bp):
CCCTACGTGGCGTATAGCGCGGACCAGGGGCCGCGCTATAC
Found at i:885218 original size:18 final size:19
Alignment explanation
Indices: 885182--885219 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
885172 AATACTATAT
* *
885182 AAAATATTATTTTTTATTA
1 AAAATATTATATTTCATTA
885201 AAAATATTA-ATTTCATTA
1 AAAATATTATATTTCATTA
885219 A
1 A
885220 TTAATCGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AAAATATTATATTTCATTA
Found at i:886138 original size:71 final size:69
Alignment explanation
Indices: 886054--886189 Score: 220
Period size: 71 Copynumber: 1.9 Consensus size: 69
886044 GCATCAAATC
* *
886054 AAAATATAAATAAGTAT-GAGCCAATTTCATATACAAATATAATTTTAATGACTAAATTGAAGTA
1 AAAATATAAATAAGTATGGA-CCAATTTCATATA-AAATAAAATTTTAAGGACTAAATTGAA-TA
886118 AATTATA
63 AATTATA
886125 AAAATATAAATAAGTATGGACCAATTTCATATAAAATAAAATTTTAAGGACTAAATTGAATAAAT
1 AAAATATAAATAAGTATGGACCAATTTCATATAAAATAAAATTTTAAGGACTAAATTGAATAAAT
886190 AAGAAATTAA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
69 5 0.08
70 25 0.40
71 30 0.48
72 2 0.03
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.32
Consensus pattern (69 bp):
AAAATATAAATAAGTATGGACCAATTTCATATAAAATAAAATTTTAAGGACTAAATTGAATAAAT
TATA
Found at i:886401 original size:23 final size:24
Alignment explanation
Indices: 886346--886402 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
886336 ATATATATTA
*
886346 TATATATAATATGTATGATGAATG
1 TATATATAATATGTATAATGAATG
*
886370 T-TATGATAATATG-ATAATGCATG
1 TATAT-ATAATATGTATAATGAATG
886393 TATATATAAT
1 TATATATAAT
886403 GTACACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (24 bp):
TATATATAATATGTATAATGAATG
Found at i:886462 original size:2 final size:2
Alignment explanation
Indices: 886443--886752 Score: 254
Period size: 2 Copynumber: 157.5 Consensus size: 2
886433 ATGCATACAT
* *
886443 TA TA AA TA TA TA CT- TA TA TA AA TA TA TA -A TA TA TA TA -A CTA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* *
886484 TA TA T- TA TA CT- TA TA -A GTA TA TA TA TA CT- TA TA CA TA TG
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA
** * * *
886523 TA TA CT- TA TA CC TA TA TA TA TA TA TA TA -A T- TA CA CA CA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
886563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GTA TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
** * * *
886605 TA TA TA GG TA TG TA TA TA -A TA TA TA AA TA TA TA -A GTA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
886646 GTA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
886688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GTG TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
886730 TG TG TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
886753 CATTAAACAT
Statistics
Matches: 253, Mismatches: 30, Indels: 50
0.76 0.09 0.15
Matches are distributed among these distances:
1 15 0.06
2 229 0.91
3 9 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:887372 original size:24 final size:24
Alignment explanation
Indices: 887331--887376 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 24
887321 ATCTTCTGAA
887331 TATATTTTAAAATTTTAAGTTAAAC
1 TATATTTTAAAATTTTAA-TTAAAC
887356 TATA-TTT-AAATTATTAATTAA
1 TATATTTTAAAATT-TTAATTAA
887377 TTAATACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TATATTTTAAAATTTTAATTAAAC
Found at i:887515 original size:14 final size:12
Alignment explanation
Indices: 887481--887519 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
887471 TTAATTTACT
887481 GATTATAATTAA
1 GATTATAATTAA
887493 GATTTATAATATAAA
1 GA-TTATAAT-T-AA
887508 GATTATAATTAA
1 GATTATAATTAA
887520 TATAGAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 4 0.17
13 8 0.33
14 8 0.33
15 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
GATTATAATTAA
Found at i:889020 original size:67 final size:67
Alignment explanation
Indices: 888940--889102 Score: 184
Period size: 67 Copynumber: 2.4 Consensus size: 67
888930 CTCGACTCGA
* * *
888940 CTCGACTCGTTGCTCATTAAGCTTGTTAAAATTTTACTCAACTCGTGCTCATTAAGAAAAATTT-
1 CTCGACTTGTTGCTCATTAAGCTCGTTAAAATTTTACTCAACTCGTGCTCACTAA-AAAAATTTG
889004 TTG
65 TTG
* * * ** ** *
889007 CTCGACTTATTGCTCATTAAACTCGTTAAAATTTTGCTTGACTCGTGCTTGCTAATAAAATTTGT
1 CTCGACTTGTTGCTCATTAAGCTCGTTAAAATTTTACTCAACTCGTGCTCACTAAAAAAATTTGT
889072 TG
66 TG
* * *
889074 CTCGATTTGTTGCTCGTTAAGCTCATTAA
1 CTCGACTTGTTGCTCATTAAGCTCGTTAA
889103 GTTCGTTGCT
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
66 7 0.09
67 72 0.91
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (67 bp):
CTCGACTTGTTGCTCATTAAGCTCGTTAAAATTTTACTCAACTCGTGCTCACTAAAAAAATTTGT
TG
Found at i:891714 original size:37 final size:36
Alignment explanation
Indices: 891654--891775 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 36
891644 TTATCCCATT
* *
891654 ATCA-TTTTC-AACAAACATCTACCAAACTTTGAAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTG-AAA
*
891689 ATTATTTTTCAAAGAAACATTTACCAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
* *
891725 ACCA-TTTTCAAAAAAAACATTTACCAAACTTTGAAA
1 ATCATTTTTC-AAAGAAACATTTACCAAACTTTGAAA
891761 ATCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
891776 TTGGTTGACA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
35 8 0.11
36 38 0.51
37 23 0.31
38 5 0.07
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATTTACCAAACTTTGAAA
Found at i:891730 original size:21 final size:21
Alignment explanation
Indices: 891703--891767 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
891693 TTTTTCAAAG
891703 AAACATTTACCAAACTTTGAA
1 AAACATTTACCAAACTTTGAA
* *
891724 AACCATTT-TCAAA-----AA
1 AAACATTTACCAAACTTTGAA
891739 AAACATTTACCAAACTTTGAA
1 AAACATTTACCAAACTTTGAA
*
891760 AATCATTT
1 AAACATTT
891768 TTTCAAAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 9 0.27
16 4 0.12
20 4 0.12
21 16 0.48
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (21 bp):
AAACATTTACCAAACTTTGAA
Found at i:897641 original size:20 final size:20
Alignment explanation
Indices: 897604--897642 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
897594 AGATTGAGTG
* * *
897604 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
897624 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
897643 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:897848 original size:20 final size:20
Alignment explanation
Indices: 897802--897862 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
897792 AGAACCCCAT
*
897802 GGGGGTATCGATTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AA
*
897825 GGGGGAATCGGTTCCCTCAA
1 GGGGGAATCGATTCCCTCAA
*
897845 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
897863 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 18 0.53
21 2 0.06
22 3 0.09
23 11 0.32
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAA
Found at i:909178 original size:32 final size:32
Alignment explanation
Indices: 909109--909170 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
909099 AGTCTAGTTT
* * * *
909109 AAATAATTTAGGTTTTAGATTTAAAATAATTC
1 AAATAATCTAAGTTTTAAATTTAAAATAATAC
909141 AAATAATCTAAGTTTTAAATTTAAAA-AATA
1 AAATAATCTAAGTTTTAAATTTAAAATAATA
909171 AGAAATAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 3 0.12
32 23 0.88
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.40
Consensus pattern (32 bp):
AAATAATCTAAGTTTTAAATTTAAAATAATAC
Found at i:920787 original size:102 final size:102
Alignment explanation
Indices: 920611--920814 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
920601 AAGAGTAGGG
920611 AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAGCATGTGCACGTGATACAGTTAGTTGT
1 AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAGCATGTGCACGTGATACAGTTAGTTGT
920676 TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
66 TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
*
920713 AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAGCATGTGCACGTGATACGGTTAGTTGT
1 AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAGCATGTGCACGTGATACAGTTAGTTGT
920778 TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
66 TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
920815 GACTTCACAA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (102 bp):
AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAGCATGTGCACGTGATACAGTTAGTTGT
TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
Found at i:925427 original size:102 final size:102
Alignment explanation
Indices: 925251--925454 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
925241 AAGAGTAGGG
*
925251 AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAGCATGTGCACGTGATACGGTTAGTTGT
1 AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAACATGTGCACGTGATACGGTTAGTTGT
925316 TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
66 TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
925353 AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAACATGTGCACGTGATACGGTTAGTTGT
1 AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAACATGTGCACGTGATACGGTTAGTTGT
925418 TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
66 TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
925455 GACTTCACAA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (102 bp):
AGAATATTAGACTATTTTGTATTTTGATATCCTATTCAACATGTGCACGTGATACGGTTAGTTGT
TGCCAGGTTGTTAGCTAGGTTGTTAGGCTAACTAACC
Found at i:932273 original size:87 final size:87
Alignment explanation
Indices: 932126--932359 Score: 312
Period size: 88 Copynumber: 2.7 Consensus size: 87
932116 GGTAAGACCT
* * **
932126 TACGGACCTAAGGATACTC-TTGGGTAGTCCCATAGGCCCCAAGGCATATTATTAGGTTGGTTCT
1 TACGGATCTAAGGATAC-CATTGGGTAG-GCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCT
*
932190 CTTTCCTGTG-GCTTAGGGTAGCGC
64 CTTTCCTGTGTGCTTAGGGTAAC-C
932214 TACGGATCTAAGGATACCATTGGGTAGGCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCTCT
1 TACGGATCTAAGGATACCATTGGGTAGGCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCTCT
**
932279 TTGTTGTGTGCTTAGGGTAACC
66 TTCCTGTGTGCTTAGGGTAACC
* * *
932301 TCACGGATCTAAGGATACCATTGGTTAGGCCCATA-GCCCCAAAGAATATCCTTAGGTTG
1 T-ACGGATCTAAGGATACCATTGGGTAGG-CCATAGGCCCCAAGGCATATCCTTAGGTTG
932360 TCCCTTGCTA
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
87 44 0.33
88 83 0.63
89 5 0.04
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (87 bp):
TACGGATCTAAGGATACCATTGGGTAGGCCATAGGCCCCAAGGCATATCCTTAGGTTGGTTCTCT
TTCCTGTGTGCTTAGGGTAACC
Found at i:934785 original size:20 final size:21
Alignment explanation
Indices: 934760--934798 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
934750 TTTAGAATAA
934760 TTTACAT-ATAATCCCTAATC
1 TTTACATGATAATCCCTAATC
*
934780 TTTACATGTTAATCCCTAA
1 TTTACATGATAATCCCTAA
934799 AAGTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (21 bp):
TTTACATGATAATCCCTAATC
Found at i:935032 original size:358 final size:353
Alignment explanation
Indices: 934206--935185 Score: 1226
Period size: 357 Copynumber: 2.7 Consensus size: 353
934196 ATCAGATTTC
* * * * * *
934206 ATTATACCAACTTAATATTGATACTATATTTGAACCATAGATATTGTATGAACAGTT-TGGTAGT
1 ATTACACCAACTTAATATTGATACTATATTTGAACTATCGACATTGTATGAACAATTATTGTA-T
*
934270 -CATTCAATGGTATTGATACCATTAGTATAAAATATGTAAATATACAATTAGTCCCTGGATTATG
65 CCATTCAATGGTATTGATACCATTAGTATAAAATAT-AAAATATACAATTAGTCCCTGGA-TATG
* * ** *
934334 TATTACTCATGCTAAGACCTTTAAAGTAGTGATATAGTATGTAATTGTTAATAGAATCGGTCTTC
128 TATTACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAACTGTTAATAGAATTAGTCTTT
* * ** *** * *
934399 AGAATAATTTA-TTACAACCCTCTTTTATATAATTACATGCCCATCCCTAAAAGTTTGTAAAGTA
193 AGAATAATTTACATACAATCC-C---TA-ATCTTTACATGTTAATCCCTAAAAGTTTGAAAAGTC
* *
934463 TT-AATTGGTCCTTGTCATATCAAAGTATAACATTAGTAATATGATGATATATAATTTAAAATCA
253 TTAAATTAGTCCTTGTCATATCAAAGTATAACATTAGCAATATGATGATATATAATTTAAAATCA
934527 ATAATTAAATGTTCGTTTAGCAAGGTATGATCAATT
318 ATAATTAAATGTTCGTTTAGCAAGGTATGATCAATT
* *
934563 ATTACACCAACTTAATATTGATA-TTTATTCGAACTATCGATC-TTGTATGAAC-ATTATTGGTA
1 ATTACACCAACTTAATATTGATACTATATTTGAACTATCGA-CATTGTATGAACAATTATT-GTA
* * * *
934625 CCCATTCAACGGTATTGATACCAATAGTATAAAATATACAATTATACAATTAGTCCCTGGATCAT
64 TCCATTCAATGGTATTGATACCATTAGTATAAAATATA-AAATATACAATTAGTCCCTGGAT-AT
*
934690 GTATTACTCATGCTAAGACCTTTTAAGTAGTGATACAGTATGTAA-T-TT-ATAGAATTAGTCTT
127 GTATTACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAACTGTTAATAGAATTAGTCTT
*
934752 TAGAATAATTTACATATAATCCCTAATCTTTACATGTTAATCCCTAAAAGTTTGAAAAGTCTTAA
192 TAGAATAATTTACATACAATCCCTAATCTTTACATGTTAATCCCTAAAAGTTTGAAAAGTCTTAA
* **
934817 ATTAGTCCTTGTCATATCAAATTAAAGTATAGCATTAGCGTTATGATGATATATATGATTTAAAA
257 ATTAGTCCTTGTCATATC-----AAAGTATAACATTAGCAATATGATGATATATA--ATTTAAAA
* * *
934882 TGAGTAATTAAATGTTTGTTTAGCAAGGTATGATCAATT
315 TCAATAATTAAATGTTCGTTTAGCAAGGTATGATCAATT
934921 ATTACACCAACTTAATATTGATACTATATTTGAACTATCGACATTGTATGAACAATTATTGTATC
1 ATTACACCAACTTAATATTGATACTATATTTGAACTATCGACATTGTATGAACAATTATTGTATC
* * * * * *
934986 CATTCAATAGTATCGATAACATTAGTATAAAATATAAAAAATACAATTAGTCCCTAGAT-TATAT
66 CATTCAATGGTATTGATACCATTAGTATAAAATATAAAATATACAATTAGTCCCTGGATATGTAT
*
935050 TACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAACTGTTAATGGAATTAGTCTTTAGA
131 TACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAACTGTTAATAGAATTAGTCTTTAGA
935115 ATAATTTACTATACAATCCCTAATCTTTTAGATAATTACATGTTAATCCCTAAAAGTTTGAAAAG
196 ATAATTTAC-ATACAATCCCTAATC-------T--TTACATGTTAATCCCTAAAAGTTTGAAAAG
935180 TCTTAA
251 TCTTAA
935186 TGTAACACCC
Statistics
Matches: 541, Mismatches: 51, Indels: 50
0.84 0.08 0.08
Matches are distributed among these distances:
350 31 0.06
351 20 0.04
354 24 0.04
355 10 0.02
356 98 0.18
357 125 0.23
358 90 0.17
359 86 0.16
360 20 0.04
367 1 0.00
369 36 0.07
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (353 bp):
ATTACACCAACTTAATATTGATACTATATTTGAACTATCGACATTGTATGAACAATTATTGTATC
CATTCAATGGTATTGATACCATTAGTATAAAATATAAAATATACAATTAGTCCCTGGATATGTAT
TACTCATGCTAAGACCTTTTAAGTAGTGATATAGTATGTAACTGTTAATAGAATTAGTCTTTAGA
ATAATTTACATACAATCCCTAATCTTTACATGTTAATCCCTAAAAGTTTGAAAAGTCTTAAATTA
GTCCTTGTCATATCAAAGTATAACATTAGCAATATGATGATATATAATTTAAAATCAATAATTAA
ATGTTCGTTTAGCAAGGTATGATCAATT
Found at i:935955 original size:30 final size:30
Alignment explanation
Indices: 935919--935990 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
935909 CCCGCAGGAC
*
935919 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
935949 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
935979 CTGTCCATAGGT
1 CTATCCAGAGGT
935991 TTCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:936015 original size:31 final size:30
Alignment explanation
Indices: 935977--936147 Score: 123
Period size: 31 Copynumber: 5.5 Consensus size: 30
935967 GATCCTCGGC
* *
935977 AACTGTCCATAGGTTTCGAAGAACCTAGGT
1 AACTGTCCATATGTTTCGAAGAACATAGGT
* **
936007 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATATGTTTCGAAGAACATAGGT
*
936038 ATACTGTCCATATGTCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTTCGAAGA-ACATAGGT
* * ** *
936069 AATTTATCCATATG-TTCTTTATAACATAGGT
1 AA-CTGTCCATATGTTTC-GAAGAACATAGGT
* *
936100 ATATTGTCCATATGTCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTTCGAAGA-ACATAGGT
936131 AATTCTGTCCATATGTT
1 AA--CTGTCCATATGTT
936148 CCTTAGAAAT
Statistics
Matches: 110, Mismatches: 20, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
30 7 0.06
31 88 0.80
32 15 0.14
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (30 bp):
AACTGTCCATATGTTTCGAAGAACATAGGT
Found at i:936079 original size:62 final size:63
Alignment explanation
Indices: 936013--936165 Score: 256
Period size: 62 Copynumber: 2.5 Consensus size: 63
936003 AGGTGAACTG
936013 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT-TA
1 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTCTA
* * * *
936075 TCCATATGTTCTTTATAACATAGGTATATTGTCCATATGTCTCGAAAGACATAGGTAATTCTG
1 TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTCTA
936138 TCCATATGTTCCTTAGAA-ATAGGTATAC
1 TCCATATGTTCCTTAGAACATAGGTATAC
936166 CCTCAACTCT
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
62 66 0.80
63 17 0.20
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (63 bp):
TCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATTCTA
Found at i:936145 original size:32 final size:30
Alignment explanation
Indices: 936030--936146 Score: 128
Period size: 31 Copynumber: 3.7 Consensus size: 30
936020 GTTCCTTAGA
*
936030 ACATAGGTATACTGTCCATATGTCTCGAAAG
1 ACATAGGTAT-TTGTCCATATGTCTCGAAAG
* ** *
936061 ACATAGGTAATTTATCCATATGTTCTTTATA-
1 ACATAGGT-ATTTGTCCATATG-TCTCGAAAG
936092 ACATAGGTATATTGTCCATATGTCTCGAAAG
1 ACATAGGTAT-TTGTCCATATGTCTCGAAAG
936123 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATT-TGTCCATATGT
936147 TCCTTAGAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
30 7 0.10
31 44 0.62
32 20 0.28
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (30 bp):
ACATAGGTATTTGTCCATATGTCTCGAAAG
Found at i:936160 original size:31 final size:31
Alignment explanation
Indices: 936010--936162 Score: 125
Period size: 31 Copynumber: 4.9 Consensus size: 31
936000 CCTAGGTGAA
*
936010 CTGTCCATATGTTCCTTAGAACATAGGT-ATA
1 CTGTCCATATGTTCCTTAGAA-ATAGGTAATT
*** *
936041 CTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGT-TCCTTAGAAATAGGTAATT
* * *
936073 -TATCCATATGTTCTTTATAACATAGGT-ATAT
1 CTGTCCATATGTTCCTTAGAA-ATAGGTAAT-T
*** *
936104 -TGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGT-TCCTTAGAAATAGGTAATT
936135 CTGTCCATATGTTCCTTAGAAATAGGTA
1 CTGTCCATATGTTCCTTAGAAATAGGTA
936163 TACCCTCAAC
Statistics
Matches: 94, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
30 6 0.06
31 64 0.68
32 24 0.26
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (31 bp):
CTGTCCATATGTTCCTTAGAAATAGGTAATT
Found at i:955191 original size:27 final size:29
Alignment explanation
Indices: 955148--955220 Score: 123
Period size: 27 Copynumber: 2.6 Consensus size: 29
955138 ACCCAAACTA
*
955148 AATGATGTCATTACTTACATCATTTAA-T
1 AATGATGTCATTGCTTACATCATTTAATT
955176 AA-GATGTCATTGCTTACATCATTTAATT
1 AATGATGTCATTGCTTACATCATTTAATT
955204 AATGATGTCATTGCTTA
1 AATGATGTCATTGCTTA
955221 TCAATTTAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 23 0.55
28 5 0.12
29 14 0.33
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (29 bp):
AATGATGTCATTGCTTACATCATTTAATT
Found at i:957525 original size:14 final size:14
Alignment explanation
Indices: 957502--957532 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
957492 TGGGCTAAAT
*
957502 ATAAATGAACGAAC
1 ATAAACGAACGAAC
957516 ATAAACGAACGAAC
1 ATAAACGAACGAAC
957530 ATA
1 ATA
957533 TTAGAGAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.16, G:0.13, T:0.13
Consensus pattern (14 bp):
ATAAACGAACGAAC
Found at i:959533 original size:23 final size:23
Alignment explanation
Indices: 959504--959588 Score: 125
Period size: 23 Copynumber: 3.7 Consensus size: 23
959494 TTCATTTATG
* * *
959504 TTCGTTTATATTCATTTATTGTG
1 TTCGTTTATGTTCGTTTATTGTA
* *
959527 TTTGTTTACGTTCGTTTATTGTA
1 TTCGTTTATGTTCGTTTATTGTA
959550 TTCGTTTATGTTCGTTTATTGTA
1 TTCGTTTATGTTCGTTTATTGTA
959573 TTCGTTTATGTTCGTT
1 TTCGTTTATGTTCGTT
959589 CATTTGTGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.61
Consensus pattern (23 bp):
TTCGTTTATGTTCGTTTATTGTA
Found at i:959553 original size:13 final size:13
Alignment explanation
Indices: 959537--959581 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
959527 TTTGTTTACG
959537 TTCGTTTATTGTA
1 TTCGTTTATTGTA
959550 TTCGTTTA-TG--
1 TTCGTTTATTGTA
959560 TTCGTTTATTGTA
1 TTCGTTTATTGTA
959573 TTCGTTTAT
1 TTCGTTTAT
959582 GTTCGTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.28
11 2 0.07
12 2 0.07
13 17 0.59
ACGTcount: A:0.13, C:0.09, G:0.16, T:0.62
Consensus pattern (13 bp):
TTCGTTTATTGTA
Found at i:959563 original size:10 final size:10
Alignment explanation
Indices: 959488--959588 Score: 67
Period size: 10 Copynumber: 9.2 Consensus size: 10
959478 GAAGAAAAAA
* *
959488 TTTATTTTCA
1 TTTATGTTCG
959498 TTTATGTTCG
1 TTTATGTTCG
* *
959508 TTTATATTCA
1 TTTATGTTCG
*
959518 TTTATTGTGTTTG
1 TTTA---TGTTCG
*
959531 TTTACGTTCG
1 TTTATGTTCG
959541 TTTATTGTATTCG
1 TTTA-TG--TTCG
959554 TTTATGTTCG
1 TTTATGTTCG
959564 TTTATTGTATTCG
1 TTTA-TG--TTCG
959577 TTTATGTTCG
1 TTTATGTTCG
959587 TT
1 TT
959589 CATTTGTGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
10 42 0.58
11 3 0.04
12 4 0.06
13 23 0.32
ACGTcount: A:0.14, C:0.09, G:0.15, T:0.62
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:962439 original size:17 final size:17
Alignment explanation
Indices: 962417--962456 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
962407 ATTTAACCAT
* *
962417 ATATATAATATTCTTTC
1 ATATATAATATTATTTA
*
962434 ATATATAATGTTATTTA
1 ATATATAATATTATTTA
962451 ATATAT
1 ATATAT
962457 CAAATACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATATAATATTATTTA
Found at i:963865 original size:23 final size:21
Alignment explanation
Indices: 963836--963888 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 21
963826 CACCAGATGC
963836 TAATATTTAGATTTTCTTTGTTG
1 TAATATTTAGATTTTC-TT-TTG
963859 TAATATTTTAGATTTTCTTTTG
1 TAATA-TTTAGATTTTCTTTTG
963881 TAATATTT
1 TAATATTT
963889 TAGTTATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.10
22 8 0.28
23 7 0.24
24 11 0.38
ACGTcount: A:0.25, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
TAATATTTAGATTTTCTTTTG
Found at i:963884 original size:22 final size:24
Alignment explanation
Indices: 963836--963891 Score: 91
Period size: 22 Copynumber: 2.5 Consensus size: 24
963826 CACCAGATGC
963836 TAATA-TTTAGATTTTCTTTGTTG
1 TAATATTTTAGATTTTCTTTGTTG
963859 TAATATTTTAGATTTTC-TT-TTG
1 TAATATTTTAGATTTTCTTTGTTG
963881 TAATATTTTAG
1 TAATATTTTAG
963892 TTATTGGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.44
23 7 0.22
24 11 0.34
ACGTcount: A:0.25, C:0.04, G:0.11, T:0.61
Consensus pattern (24 bp):
TAATATTTTAGATTTTCTTTGTTG
Found at i:968340 original size:59 final size:57
Alignment explanation
Indices: 968246--968357 Score: 136
Period size: 59 Copynumber: 1.9 Consensus size: 57
968236 AAAAGATATC
* * *
968246 ATTTAATTTGAATATTAGTAGGATAATTATTCTTTTGAATATGTCAAACTAAATAAGT
1 ATTTAATTTGAATATTAG-AAGATAATTATACTTTTAAATATGTCAAACTAAATAAGT
* *
968304 ATTTAACTTTGAATATTA-AAGATAAGTATATACTTTTAAATATTTCAAATTAAA
1 ATTTAA-TTTGAATATTAGAAGATAA-T-TATACTTTTAAATATGTCAAACTAAA
968358 ATAATATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
57 6 0.13
58 7 0.15
59 33 0.72
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (57 bp):
ATTTAATTTGAATATTAGAAGATAATTATACTTTTAAATATGTCAAACTAAATAAGT
Found at i:969652 original size:19 final size:19
Alignment explanation
Indices: 969580--969673 Score: 65
Period size: 19 Copynumber: 5.1 Consensus size: 19
969570 TATTTTGAAT
969580 AATTTATTTATTTATTT-A
1 AATTTATTTATTTATTTCA
* *
969598 ATATTTTTTTGATTGA-TT--
1 A-ATTTATTT-ATTTATTTCA
* * *
969616 GATTTATTTAGTTGTTTCA
1 AATTTATTTATTTATTTCA
969635 AATTTATTTATTTATTTCGA
1 AATTTATTTATTTATTTC-A
969655 AA-TTA-TTAGTTTATTTCA
1 AATTTATTTA-TTTATTTCA
969673 A
1 A
969674 GAGATATGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
16 2 0.03
17 9 0.15
18 6 0.10
19 35 0.59
20 7 0.12
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.61
Consensus pattern (19 bp):
AATTTATTTATTTATTTCA
Found at i:972575 original size:14 final size:14
Alignment explanation
Indices: 972558--972588 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
972548 AATAAGTGAA
972558 AATGAAATAATGCT
1 AATGAAATAATGCT
972572 AATGAAATAATGCT
1 AATGAAATAATGCT
972586 AAT
1 AAT
972589 TACAACTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (14 bp):
AATGAAATAATGCT
Found at i:978708 original size:2 final size:2
Alignment explanation
Indices: 978701--978731 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
978691 ATTTTAAAAC
978701 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 A
978732 CCCCTATCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:978919 original size:12 final size:12
Alignment explanation
Indices: 978894--978986 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
978884 ACGGAGATAT
* *
978894 CAGAAATCAAAA
1 CAGAATTCAGAA
978906 CAGAATTCAGAA
1 CAGAATTCAGAA
978918 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
*
978930 CAGAATCCAGATA
1 CAGAATTCAGA-A
*
978943 -AGAAATCAGAA
1 CAGAATTCAGAA
* **
978954 CAAAATTCAGGT
1 CAGAATTCAGAA
*
978966 CA-TATATCAGAA
1 CAGAAT-TCAGAA
978978 CAGAATTCA
1 CAGAATTCA
978987 AGTCAGAAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
11 5 0.08
12 52 0.84
13 5 0.08
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:978921 original size:24 final size:24
Alignment explanation
Indices: 978894--979000 Score: 101
Period size: 24 Copynumber: 4.5 Consensus size: 24
978884 ACGGAGATAT
*
978894 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* *
978918 CAGATATCAGAACAGAATCCAGATA
1 CAGAAATCAGAACAGAATTCAGA-A
* **
978943 -AGAAATCAGAACAAAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
* * *
978966 CATATATCAGAACAGAATTCA-AGT
1 CAGAAATCAGAACAGAATTCAGA-A
978990 CAGAAATCAGA
1 CAGAAATCAGA
979001 TAAAATATTT
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
24 65 0.98
25 1 0.02
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:978961 original size:48 final size:48
Alignment explanation
Indices: 978895--979000 Score: 133
Period size: 48 Copynumber: 2.2 Consensus size: 48
978885 CGGAGATATC
* *
978895 AGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCC-AGATA
1 AGAAATCAGAACAAAATTCAGAACAGATATCAGAACAGAATCCAAG-TA
** * * *
978943 AGAAATCAGAACAAAATTCAGGTCATATATCAGAACAGAATTCAAGTC
1 AGAAATCAGAACAAAATTCAGAACAGATATCAGAACAGAATCCAAGTA
978991 AGAAATCAGA
1 AGAAATCAGA
979001 TAAAATATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
48 48 0.96
49 2 0.04
ACGTcount: A:0.52, C:0.16, G:0.15, T:0.17
Consensus pattern (48 bp):
AGAAATCAGAACAAAATTCAGAACAGATATCAGAACAGAATCCAAGTA
Found at i:979575 original size:17 final size:17
Alignment explanation
Indices: 979549--979591 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
979539 GAGTTTCCAA
*
979549 ACTTATTCCAATCTCTT
1 ACTTAATCCAATCTCTT
979566 ACTTAATCCAATCTCTT
1 ACTTAATCCAATCTCTT
979583 ACTTAATCC
1 ACTTAATCC
979592 TCAGTCTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (17 bp):
ACTTAATCCAATCTCTT
Found at i:983597 original size:25 final size:25
Alignment explanation
Indices: 983563--983631 Score: 129
Period size: 25 Copynumber: 2.8 Consensus size: 25
983553 TGCTTCAATC
*
983563 CATCTTTACATCCATTTTTTTGTTA
1 CATCTTTACATCCATTTTTTGGTTA
983588 CATCTTTACATCCATTTTTTGGTTA
1 CATCTTTACATCCATTTTTTGGTTA
983613 CATCTTTACATCCATTTTT
1 CATCTTTACATCCATTTTT
983632 AGAATCCAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.20, C:0.22, G:0.04, T:0.54
Consensus pattern (25 bp):
CATCTTTACATCCATTTTTTGGTTA
Found at i:983803 original size:30 final size:30
Alignment explanation
Indices: 983768--983830 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
983758 ATGATGATAT
*
983768 TTGAATTTTATTTTGACTGCATTATTTTAA
1 TTGAATTTTAATTTGACTGCATTATTTTAA
*
983798 TTGAATTTTAATTTGACTGCATTATTTTTA
1 TTGAATTTTAATTTGACTGCATTATTTTAA
983828 TTG
1 TTG
983831 CAAGGTAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.06, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGAATTTTAATTTGACTGCATTATTTTAA
Found at i:996687 original size:20 final size:20
Alignment explanation
Indices: 996658--996695 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
996648 TTTCAAAGTG
996658 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
996678 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
996696 TAATTTTTCA
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:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:996772 original size:45 final size:46
Alignment explanation
Indices: 996718--996805 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
996708 CATTGAATGT
* *
996718 ATTTTATGCATCGATGCAC-ATACCATGCATCGACGCACTCAGTGC
1 ATTTGATGCATCGATGCACAAGACCATGCATCGACGCACTCAGTGC
*
996763 ATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1 ATTTGATGCATCGATGCACAAGACCATGCATCGACGCACTCAG
996806 GTTTTTCAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 18 0.46
46 21 0.54
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (46 bp):
ATTTGATGCATCGATGCACAAGACCATGCATCGACGCACTCAGTGC
Found at i:996821 original size:46 final size:45
Alignment explanation
Indices: 996726--996827 Score: 107
Period size: 46 Copynumber: 2.2 Consensus size: 45
996716 GTATTTTATG
* * **
996726 CATCGATGCACATACCATGCATCGACGCACTCAGTGCATTTGATG
1 CATCGATGCACAGACCATGCATCGACGCACTCAGTGCATTTAAAA
* **
996771 CATCGATGCACAAGACCATGCATCGATGCACTCAG-GTTTTTCAAAA
1 CATCGATGCAC-AGACCATGCATCGACGCACTCAGTGCATTT-AAAA
996817 CATCGAATGCA
1 CATCG-ATGCA
996828 TTTTATGCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
45 15 0.32
46 27 0.57
47 5 0.11
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (45 bp):
CATCGATGCACAGACCATGCATCGACGCACTCAGTGCATTTAAAA
Done.