Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008002.1 Hibiscus syriacus cultivar Beakdansim tig00110461_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: 1031338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:760575 original size:2 final size:2
Alignment explanation
Indices: 760568--760620 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
760558 AGTATACGTG
760568 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
760610 AT AT AT AT AT A
1 AT AT AT AT AT A
760621 AAGTTATTGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:761003 original size:30 final size:30
Alignment explanation
Indices: 760942--761071 Score: 170
Period size: 30 Copynumber: 4.3 Consensus size: 30
760932 CTAAGGAACA
* * ***
760942 TATGGATAGTTTACCTAGGTTCTTCGGGACC
1 TATGGATAG-TTACCGAGGATCTTTATGACC
*
760973 TATGGATATTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
761003 TATGGATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
* *
761033 TCTGAATAGTTACCGAGGATCTTTATGACC
1 TATGGATAGTTACCGAGGATCTTTATGACC
*
761063 TCTGGATAG
1 TATGGATAG
761072 GTCATTCGGG
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 81 0.91
31 8 0.09
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (30 bp):
TATGGATAGTTACCGAGGATCTTTATGACC
Found at i:763015 original size:60 final size:59
Alignment explanation
Indices: 762919--763036 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
762909 CTCTACAATG
* * * *
762919 TCGACATTTAGGTCGAACAAGCTGGTAGTTGCATGTCTTTCCCTT-GAACTTGAAGGCATA
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGTC--TCCCTTAGAACTTGAAGGCATA
* *
762979 TCGACATTGAGGTCGAAGAAGCTCGCAGTTGAATGTCTCCCTTAGAGCTTGAAGGCAT
1 TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGTCTCCCTTAGAACTTGAAGGCAT
763037 CGTGTCAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 6 0.12
59 13 0.25
60 32 0.63
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (59 bp):
TCGACATTGAGGTCGAACAAGCTCGCAGTTGAATGTCTCCCTTAGAACTTGAAGGCATA
Found at i:764016 original size:24 final size:25
Alignment explanation
Indices: 763989--764056 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 25
763979 ACATTACAAT
*
763989 AAAAATAGAAGGAATTGATGAAG-C
1 AAAAATAGAAGGAATTGATGAAGTA
*
764013 AAAAATTGAAGGAATTGATGAAGTA
1 AAAAATAGAAGGAATTGATGAAGTA
*
764038 AAAAATAGAAAGAATTGAT
1 AAAAATAGAAGGAATTGAT
764057 TTGATGATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 22 0.56
25 17 0.44
ACGTcount: A:0.56, C:0.01, G:0.22, T:0.21
Consensus pattern (25 bp):
AAAAATAGAAGGAATTGATGAAGTA
Found at i:764388 original size:29 final size:28
Alignment explanation
Indices: 764328--764388 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
764318 GATTAACACT
*
764328 TTATT-AGAAAAGGTGTTAGATAGATAA
1 TTATTAAGAAAAGGTGTTAGACAGATAA
*
764355 -AATTAAGAAAAAGAGTGTT-GACAGATAA
1 TTATTAAG-AAAAG-GTGTTAGACAGATAA
764383 TTATTA
1 TTATTA
764389 TCTGGGTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
26 3 0.11
27 2 0.07
28 13 0.48
29 9 0.33
ACGTcount: A:0.48, C:0.02, G:0.20, T:0.31
Consensus pattern (28 bp):
TTATTAAGAAAAGGTGTTAGACAGATAA
Found at i:779258 original size:20 final size:20
Alignment explanation
Indices: 779210--779465 Score: 90
Period size: 20 Copynumber: 12.5 Consensus size: 20
779200 AATGACCAAT
*
779210 AAAATCGCAACGCGA-T-ATC
1 AAAATCGCAACGCGATTGA-G
*
779229 AAAATTGCAACGCGATTGAG
1 AAAATCGCAACGCGATTGAG
** ***
779249 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTGAG
**
779269 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TGAG
* **
779289 AAAATCGTAACGCGAGCTT-CC
1 AAAATCGCAACGCGA--TTGAG
**
779310 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* *
779333 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
* * * *
779353 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTGAG
* *
779373 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* * * *
779393 AGAGTCGCAACGTGATTTAGAAT
1 AAAATCGCAACGCGA-TT-G-AG
* *
779416 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* * *
779436 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
*
779456 AGAATCGCAA
1 AAAATCGCAA
779466 TACGATTTAT
Statistics
Matches: 184, Mismatches: 39, Indels: 27
0.74 0.16 0.11
Matches are distributed among these distances:
19 14 0.08
20 123 0.67
21 18 0.10
22 4 0.02
23 24 0.13
24 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTGAG
Found at i:779423 original size:83 final size:83
Alignment explanation
Indices: 779314--779488 Score: 251
Period size: 83 Copynumber: 2.1 Consensus size: 83
779304 GCTTCCAAGT
* * * * * *
779314 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGTGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* *
779379 GCAATGCGATTGAGAGAG
66 GCAATACGATTGAGAGAA
*
779397 TCGCAACGTGATTTAGAATAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGTGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
* *
779462 GCAATACGATTTATAGAA
66 GCAATACGATTGAGAGAA
779480 TCGCAACGT
1 TCGCAACGT
779489 TGAAAATTGC
Statistics
Matches: 81, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (83 bp):
TCGCAACGTGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATACGATTGAGAGAA
Found at i:779466 original size:20 final size:20
Alignment explanation
Indices: 779335--779485 Score: 167
Period size: 20 Copynumber: 7.4 Consensus size: 20
779325 TTTAGAAGAA
779335 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
*
779355 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGATAG
*
779375 AATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGATAG
* * * *
779395 AGTCGCAACGTGATTTAGAATAA
1 AATCGCAATGCGA-TT-G-ATAG
* *
779418 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGATAG
* *
779438 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGATAG
* *
779458 AATCGCAATACGATTTATAG
1 AATCGCAATGCGATTGATAG
779478 AATCGCAA
1 AATCGCAA
779486 CGTTGAAAAT
Statistics
Matches: 110, Mismatches: 18, Indels: 6
0.82 0.13 0.04
Matches are distributed among these distances:
20 93 0.85
21 3 0.03
22 2 0.02
23 12 0.11
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:779473 original size:63 final size:62
Alignment explanation
Indices: 779335--779474 Score: 176
Period size: 63 Copynumber: 2.3 Consensus size: 62
779325 TTTAGAAGAA
* * * * *
779335 AATCGCAATGCGA-TT-GATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTTAGATAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
* * *
779395 AGTCGCAACGTGATTTAGAATAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTTAG-ATAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
*
779458 AATCGCAATACGATTTA
1 AATCGCAATGCGATTTA
779475 TAGAATCGCA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
60 10 0.15
61 2 0.03
62 1 0.02
63 52 0.80
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (62 bp):
AATCGCAATGCGATTTAGATAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
Found at i:779600 original size:6 final size:6
Alignment explanation
Indices: 779589--779723 Score: 263
Period size: 6 Copynumber: 22.7 Consensus size: 6
779579 AGACACGTAT
779589 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
779637 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
779685 GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC
779724 CGAGACGAGA
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.04
6 124 0.96
ACGTcount: A:0.33, C:0.50, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:780420 original size:6 final size:6
Alignment explanation
Indices: 780404--780447 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
780394 TCTCGTCTCG
* **
780404 GGTCG- GGTCGT GGTCGT AGTCGT GGTCGT GGTAAT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
780448 AATACGTGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.07, C:0.14, G:0.48, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:780441 original size:12 final size:12
Alignment explanation
Indices: 780426--780450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
780416 GTCGTAGTCG
780426 TGGTCGTGGTAA
1 TGGTCGTGGTAA
780438 TGGTCGTGGTAA
1 TGGTCGTGGTAA
780450 T
1 T
780451 ACGTGTCTTC
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:0.08, G:0.40, T:0.36
Consensus pattern (12 bp):
TGGTCGTGGTAA
Found at i:780569 original size:20 final size:20
Alignment explanation
Indices: 780544--780881 Score: 169
Period size: 20 Copynumber: 16.6 Consensus size: 20
780534 CCGTTGCGAA
780544 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
780564 CGTTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
780584 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
780604 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
780624 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
780644 CATTACGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
780664 CATTGCGATTTTATTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
780687 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
780707 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
780727 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
780747 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
780770 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
780791 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
780809 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
780831 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
780851 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
780870 CGTTGCGATTTT
1 CGTTGCGATTTT
780882 ATTGGTCATT
Statistics
Matches: 263, Mismatches: 44, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.06
20 196 0.75
21 14 0.05
22 6 0.02
23 28 0.11
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:780590 original size:40 final size:40
Alignment explanation
Indices: 780546--780777 Score: 257
Period size: 40 Copynumber: 5.7 Consensus size: 40
780536 GTTGCGAACG
* * * *
780546 TTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
780586 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * * *
780626 TTGCGATTCTCTCAGTCGCATTACGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
780666 TTGCGATTTTATTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TT-CTCTAAATCGCATTGCGATTCTCTCAATCGCA
* *
780709 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
*
780749 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TTC-TCTAAATCGCATTGCGA
780778 ACTTGGAAGC
Statistics
Matches: 164, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
40 111 0.68
41 2 0.01
42 5 0.03
43 46 0.28
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:780713 original size:83 final size:83
Alignment explanation
Indices: 780546--780777 Score: 281
Period size: 83 Copynumber: 2.8 Consensus size: 83
780536 GTTGCGAACG
* * * * * * * * *
780546 TTGCGATTTTCTAAATCGCGTTGCGATTCTATAAATCGCATTGCGA--TT-CTCTCAGTCGCATT
1 TTGCGATTCTATAAATCGCATTACGATTCTATCAATCGCATTGCGATTTTATTCTAAATCGCGTT
* *
780608 GCGATTCTCTCAGTCGCA
66 GCGACTCTCTCAATCGCA
* * * * *
780626 TTGCGATTCTCTCAGTCGCATTACGATTCTCTCAGTCGCATTGCGATTTTATTCTAAATCGCGTT
1 TTGCGATTCTATAAATCGCATTACGATTCTATCAATCGCATTGCGATTTTATTCTAAATCGCGTT
780691 GCGACTCTCTCAATCGCA
66 GCGACTCTCTCAATCGCA
* *
780709 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTT
1 TTGCGATTCTATAAATCGCATTACGATTCTATCAATCGCATTGCGATTTTATTCTAAATCGCGTT
780774 GCGA
66 GCGA
780778 ACTTGGAAGC
Statistics
Matches: 128, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
80 38 0.30
82 2 0.02
83 88 0.69
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (83 bp):
TTGCGATTCTATAAATCGCATTACGATTCTATCAATCGCATTGCGATTTTATTCTAAATCGCGTT
GCGACTCTCTCAATCGCA
Found at i:780871 original size:19 final size:20
Alignment explanation
Indices: 780831--780881 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
780821 TTCTTTTTAA
*
780831 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
780851 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
780870 CGTTGCGATTTT
1 CGTTGCGATTTT
780882 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:786405 original size:2 final size:2
Alignment explanation
Indices: 786390--786462 Score: 114
Period size: 2 Copynumber: 37.5 Consensus size: 2
786380 TATTTTTCAA
* *
786390 AT AT AT TT AT -T AT AT AT AT AT A- AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
786430 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 A
786463 ATCACCTAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
1 2 0.03
2 63 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:795498 original size:14 final size:15
Alignment explanation
Indices: 795481--795509 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
795471 TTTATTGTGT
795481 TATATT-TTCATTTA
1 TATATTATTCATTTA
795495 TATATTATTCATTTA
1 TATATTATTCATTTA
795510 ATCAGGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTATTCATTTA
Found at i:798652 original size:13 final size:13
Alignment explanation
Indices: 798634--798659 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
798624 CAAAAAGTAT
798634 TAAATGGTAAATG
1 TAAATGGTAAATG
798647 TAAATGGTAAATG
1 TAAATGGTAAATG
798660 ATAACCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
TAAATGGTAAATG
Found at i:801047 original size:17 final size:16
Alignment explanation
Indices: 801000--801056 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
800990 TATGTAAAAA
*
801000 ATTAATTAAA-TACAAT
1 ATTAAATAAACTA-AAT
**
801016 ATTAAATAATTTAAAT
1 ATTAAATAAACTAAAT
801032 ACTTAAATAAACTAAAT
1 A-TTAAATAAACTAAAT
*
801049 ATAAAATA
1 ATTAAATA
801057 TAAAATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 18 0.53
17 16 0.47
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
ATTAAATAAACTAAAT
Found at i:809352 original size:24 final size:24
Alignment explanation
Indices: 809325--809375 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
809315 ATCGAACCAA
*
809325 AATTTATTTGAAAATTATTAACCG
1 AATTAATTTGAAAATTATTAACCG
809349 AATTAATTTGAAAATTATTAACCG
1 AATTAATTTGAAAATTATTAACCG
809373 AAT
1 AAT
809376 CGAATTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (24 bp):
AATTAATTTGAAAATTATTAACCG
Found at i:809453 original size:137 final size:135
Alignment explanation
Indices: 809285--809579 Score: 377
Period size: 137 Copynumber: 2.2 Consensus size: 135
809275 AACGGTTAAA
* *
809285 GAAA-AAAAATT-GGTTAATTCGGTTTGGTTAATCGAACCAAAATTTATTTGAAAATTATTAA-C
1 GAAACAAAAATTCGGTTAATTTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACC
* *
809347 -C-GAATTAATTTGAAAATTATTAACCGAATCGAATTAACAT-ATTTTTTTTTGAAAATTATTAA
66 ACTGAATTAATTT-AAAACTATTAACCGAACCGAATTAAC-TGA--TTTTTTT--AAATTATTAA
809409 CCAAATTAATC
125 CCAAATTAATC
*
809420 GAAACAAAAATTCGGTTAATTTGGTTCGGTTAATCGAACTAAAATTTATTTGAAAATTATTAACC
1 GAAACAAAAATTCGGTTAATTTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACC
* * *
809485 AAACTGAATTAATTTAAAACTATTAATCGAACCGAATTAACTGATTTTTTTAAATTATTAATCGA
66 --ACTGAATTAATTTAAAACTATTAACCGAACCGAATTAACTGATTTTTTTAAATTATTAACCAA
*
809550 ATTAATT
129 ATTAATC
* *
809557 GAAGCAAAAATTCAGTTAATTTG
1 GAAACAAAAATTCGGTTAATTTG
809580 AAAATTATTA
Statistics
Matches: 141, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
135 4 0.03
136 7 0.05
137 86 0.61
138 1 0.01
139 7 0.05
140 1 0.01
141 25 0.18
142 10 0.07
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (135 bp):
GAAACAAAAATTCGGTTAATTTGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACC
ACTGAATTAATTTAAAACTATTAACCGAACCGAATTAACTGATTTTTTTAAATTATTAACCAAAT
TAATC
Found at i:809508 original size:28 final size:29
Alignment explanation
Indices: 809462--809524 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
809452 ATCGAACTAA
* * *
809462 AATTTATTTGAAAATTATTAACCAAACTG
1 AATTAATTTGAAAACTATTAACCAAACCG
* *
809491 AATTAATTT-AAAACTATTAATCGAACCG
1 AATTAATTTGAAAACTATTAACCAAACCG
809519 AATTAA
1 AATTAA
809525 CTGATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (29 bp):
AATTAATTTGAAAACTATTAACCAAACCG
Found at i:809608 original size:137 final size:134
Alignment explanation
Indices: 809312--809629 Score: 333
Period size: 137 Copynumber: 2.3 Consensus size: 134
809302 TTCGGTTTGG
* * * *
809312 TTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAATTAATTTGAAAATTATTAACCGAATC
1 TTAACCGAACTAAAATTTATTTGAAAATTATTAACCGAATTAATTTGAAAACTATTAACCGAACC
*
809377 GAATTAACATATTTTTTTTTGAAAATTATTAACCAAATTAATCGAAACAAAAATTCGGTTAATTT
66 GAATTAACATA-TTTTTTTT-AAAATTATTAACCAAATTAATCGAAACAAAAATTCAGTTAATTT
* *
809442 GGTTCGG
129 GATTC-A
* *
809449 TTAATCGAACTAAAATTTATTTGAAAATTATTAACCAAACTGAATTAATTT-AAAACTATTAATC
1 TTAACCGAACTAAAATTTATTTGAAAATTATTAA-C---C-GAATTAATTTGAAAACTATTAACC
* * * *
809513 GAACCGAATTAAC-TGA-TTTTTTT-AAATTATTAATCGAATTAATTGAAGCAAAAATTCAGTTA
61 GAACCGAATTAACAT-ATTTTTTTTAAAATTATTAACCAAATTAATCGAAACAAAAATTCAGTTA
809575 ATTTGAAAATT-A
125 ATTTG---ATTCA
* * * *
809587 TTAACCGAACT-GAATTAATTTGAAAATTATTACCCGAACTAAT
1 TTAACCGAACTAAAATTTATTTGAAAATTATTAACCGAATTAAT
809630 CGATTTTTTT
Statistics
Matches: 156, Mismatches: 16, Indels: 23
0.80 0.08 0.12
Matches are distributed among these distances:
132 7 0.04
133 1 0.01
136 1 0.01
137 91 0.58
138 11 0.07
139 7 0.04
140 3 0.02
141 25 0.16
142 10 0.06
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (134 bp):
TTAACCGAACTAAAATTTATTTGAAAATTATTAACCGAATTAATTTGAAAACTATTAACCGAACC
GAATTAACATATTTTTTTTAAAATTATTAACCAAATTAATCGAAACAAAAATTCAGTTAATTTGA
TTCA
Found at i:809672 original size:105 final size:106
Alignment explanation
Indices: 809467--809682 Score: 305
Period size: 105 Copynumber: 2.0 Consensus size: 106
809457 ACTAAAATTT
*
809467 ATTTGAAAATTATTAACCAAACTGAATTAATTTAAAACTATTAATCGAACCGAATTAACTGATTT
1 ATTTGAAAATTATTAACCAAACTGAATTAATTTAAAACTATTAATC--ACCGAACTAACTGATTT
* *
809532 TTTTAAATTATTAATCGAATTAATTGAAGCAAAAATTCAGTTA
64 TTTTAAATTATTAATCGAATTAATCGAAGAAAAAATTCAGTTA
* *
809575 ATTTGAAAATTATTAACCGAACTGAATTAATTTGAAAATTATT-A-C-CCGAACTAA-TCGATTT
1 ATTTGAAAATTATTAACCAAACTGAATTAATTT-AAAACTATTAATCACCGAACTAACT-GATTT
*
809636 TTTTAAAATTATTAATCGAATTAATCGAAGAAAAAATTCGGTTA
64 TTTT-AAATTATTAATCGAATTAATCGAAGAAAAAATTCAGTTA
809680 ATT
1 ATT
809683 CGGTTCGGTT
Statistics
Matches: 99, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
103 1 0.01
104 17 0.17
105 39 0.39
107 1 0.01
108 33 0.33
109 8 0.08
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (106 bp):
ATTTGAAAATTATTAACCAAACTGAATTAATTTAAAACTATTAATCACCGAACTAACTGATTTTT
TTAAATTATTAATCGAATTAATCGAAGAAAAAATTCAGTTA
Found at i:809713 original size:105 final size:102
Alignment explanation
Indices: 809527--809723 Score: 243
Period size: 105 Copynumber: 1.9 Consensus size: 102
809517 CGAATTAACT
* * *
809527 GATTTTTTTAAATTATTAATCGAATTAATTGAAGCAAAAATTCAGTTAATTTGAAAATTATTAAC
1 GATTTTTTTAAATTATTAATCGAATTAATCGAAGAAAAAATTCAGTTAATTCG--AATTATTAAC
**
809592 CGAACTGAATTAATTTGAAAATTATTACCCGAACTAATC
64 CGAACAAAATTAATTTGAAAATTATTACCCGAACTAATC
* * *
809631 GATTTTTTTAAAATTATTAATCGAATTAATCGAAGAAAAAATTCGGTTAATTCG-GTTCGGTTAA
1 GATTTTTTT-AAATTATTAATCGAATTAATCGAAGAAAAAATTCAGTTAATTCGAATT--ATTAA
* *
809695 TCGAACCAAAATTTATTTGAAAATTATTA
63 CCGAA-CAAAATTAATTTGAAAATTATTA
809724 ACCAAACCGA
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
102 2 0.03
104 17 0.22
105 60 0.76
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (102 bp):
GATTTTTTTAAATTATTAATCGAATTAATCGAAGAAAAAATTCAGTTAATTCGAATTATTAACCG
AACAAAATTAATTTGAAAATTATTACCCGAACTAATC
Found at i:813077 original size:2 final size:2
Alignment explanation
Indices: 813070--813103 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
813060 AGACCATTGC
813070 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
813104 CAACATTCTT
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:818620 original size:20 final size:19
Alignment explanation
Indices: 818564--818622 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
818554 TTATACTTTA
818564 TATTTAATTAAAA-ATATT
1 TATTTAATTAAAATATATT
* * *
818582 AATTAAATTAGAACT-TATT
1 TATTTAATTA-AAATATATT
818601 TATTTAATTTAAAATATATT
1 TATTTAA-TTAAAATATATT
818621 TA
1 TA
818623 AGAAATAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
18 8 0.26
19 14 0.45
20 9 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TATTTAATTAAAATATATT
Found at i:819788 original size:32 final size:34
Alignment explanation
Indices: 819752--819821 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
819742 ACCTTACAAC
*
819752 TCCCTAG-TTTTTC-CGGGATAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
* *
819784 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
819818 TCCC
1 TCCC
819822 ATTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGATAAACTAGAACCTT
Found at i:822934 original size:20 final size:20
Alignment explanation
Indices: 822909--822987 Score: 104
Period size: 20 Copynumber: 3.9 Consensus size: 20
822899 TCGTTAGACA
822909 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCT-G
*
822930 GGGGAGAATCGGTACCCCCTA
1 GGGG-GAATCGGTACCCCCTG
* *
822951 GGGGGAATCTGTTCCCCCTG
1 GGGGGAATCGGTACCCCCTG
*
822971 GGGGGAATCTGTACCCC
1 GGGGGAATCGGTACCCC
822988 TGGACAATCT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 29 0.56
21 8 0.15
22 15 0.29
ACGTcount: A:0.16, C:0.29, G:0.37, T:0.18
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCCTG
Found at i:834360 original size:3 final size:3
Alignment explanation
Indices: 834354--834396 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
834344 GAGTTTGTAA
834354 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
834397 GTTAAAGGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:835651 original size:25 final size:25
Alignment explanation
Indices: 835622--835670 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
835612 CTAAACAGTT
835622 GACAGTTCCAAAATTGGACCAGACG
1 GACAGTTCCAAAATTGGACCAGACG
835647 GACAGTTCCAAAATTGGACCAGAC
1 GACAGTTCCAAAATTGGACCAGAC
835671 AAGAGAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (25 bp):
GACAGTTCCAAAATTGGACCAGACG
Found at i:840432 original size:45 final size:45
Alignment explanation
Indices: 840361--840480 Score: 163
Period size: 45 Copynumber: 2.7 Consensus size: 45
840351 TTCGTATGTT
* *
840361 TAATCTAATATGACATCTTCAATTGTTTGCATTATCATGTGTACC
1 TAATCTGATATGACATCTTCAATTGTTTGCATTATCATATGTACC
* * * *
840406 TAATGTGATATGACATCTTCAATTGTTTGTACTATCATATGTATC
1 TAATCTGATATGACATCTTCAATTGTTTGCATTATCATATGTACC
*
840451 TAATCTG--ATGAGATCTTCAATTGTTTGCAT
1 TAATCTGATATGACATCTTCAATTGTTTGCAT
840481 GTGTGATAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 20 0.31
45 45 0.69
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (45 bp):
TAATCTGATATGACATCTTCAATTGTTTGCATTATCATATGTACC
Found at i:843363 original size:16 final size:17
Alignment explanation
Indices: 843342--843373 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
843332 AATCGTTGGA
843342 TGAGG-AAATAGATGGG
1 TGAGGAAAATAGATGGG
843358 TGAGGAAAATAGATGG
1 TGAGGAAAATAGATGG
843374 CTTAGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (17 bp):
TGAGGAAAATAGATGGG
Found at i:843641 original size:19 final size:19
Alignment explanation
Indices: 843617--843653 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
843607 ATGACCAACA
*
843617 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
843636 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
843654 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:843723 original size:20 final size:20
Alignment explanation
Indices: 843698--843750 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
843688 GATTTTAGAT
843698 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
843718 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
843738 AATCGCAATGCGA
1 AATCGCAATGCGA
843751 TAACACTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:843765 original size:21 final size:21
Alignment explanation
Indices: 843739--843789 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
843729 GAATATGTAA
*
843739 ATCGCAATGCGATAACACTTG
1 ATCGCAACGCGATAACACTTG
843760 ATCGCAACGCGATAACACTTG
1 ATCGCAACGCGATAACACTTG
843781 ATCGCAACG
1 ATCGCAACG
843790 TGATTCTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAACACTTG
Found at i:843806 original size:20 final size:20
Alignment explanation
Indices: 843781--843882 Score: 125
Period size: 20 Copynumber: 5.0 Consensus size: 20
843771 ATAACACTTG
*
843781 ATCGCAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
843801 ATCGCAACGCAATTCAGACT
1 ATCGCAACGCGATTCTGACT
**
843821 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
*
843841 GATCGCAATGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
843862 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
843882 A
1 A
843883 ACGTATCACT
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 50 0.74
21 14 0.21
22 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:843834 original size:61 final size:61
Alignment explanation
Indices: 843760--843882 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 61
843750 ATAACACTTG
* *
843760 ATCGCAACGCGATAACACTTGATCGCAACGTGATTCTGACTATCGCAACGCAATTCAGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACTATCGCAACGCAATTCAGACT
* * * *
843821 ATCGCAACGCGATAATACGTGATCGCAATGCGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACTATCGCAACGCAATTCAGACT
843882 A
1 A
843883 ACGTATCACT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (61 bp):
ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACTATCGCAACGCAATTCAGACT
Found at i:843847 original size:21 final size:20
Alignment explanation
Indices: 843739--843854 Score: 85
Period size: 21 Copynumber: 5.7 Consensus size: 20
843729 GAATATGTAA
*
843739 ATCGCAATGCGATAACACTTG
1 ATCGCAACGCGATAACAC-TG
843760 ATCGCAACGCGATAACACTTG
1 ATCGCAACGCGATAACAC-TG
* *
843781 ATCGCAACGTGAT-TCTGACT-
1 ATCGCAACGCGATAAC--ACTG
* * *
843801 ATCGCAACGCAATTCAGACT-
1 ATCGCAACGCGA-TAACACTG
*
843821 ATCGCAACGCGATAATACGTG
1 ATCGCAACGCGATAACAC-TG
*
843842 ATCGCAATGCGAT
1 ATCGCAACGCGAT
843855 TCTGACTATC
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
19 4 0.05
20 26 0.33
21 46 0.59
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAACACTG
Found at i:844727 original size:22 final size:24
Alignment explanation
Indices: 844699--844750 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
844689 GTATTCGAAA
844699 TTTGATC-TGGTCAATACT-GGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
844721 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
844745 TTTGAT
1 TTTGAT
844751 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 7 0.26
23 11 0.41
24 9 0.33
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:847225 original size:20 final size:19
Alignment explanation
Indices: 847177--847375 Score: 91
Period size: 20 Copynumber: 10.6 Consensus size: 19
847167 CATTCATTTG
*
847177 ACTATCGCAACGCGAATAG
1 ACTATCGCAACGCGAATAA
847196 ACTATCGCAACGCGAATATA
1 ACTATCGCAACGCGAATA-A
* * *
847216 ACTATTGCAACGTGAATTTGA
1 ACTATCGCAACGCGAA--TAA
*
847237 A-TATCGCAACG-GGAT--
1 ACTATCGCAACGCGAATAA
*
847252 A--ATCGCAATGCGAA-AA
1 ACTATCGCAACGCGAATAA
* **
847268 TGACTATCACAACGCGAATTTG
1 --ACTATCGCAACGCGAA-TAA
*
847290 ACTATCGCAACG-GGAT--
1 ACTATCGCAACGCGAATAA
*
847306 A--ATCGCAATGCGAA-AA
1 ACTATCGCAACGCGAATAA
*
847322 TGACTATCGCAACGCGAATTTA
1 --ACTATCGCAACGCGAA-TAA
**
847344 ACTATCGCAACGCGAATTTG
1 ACTATCGCAACGCGAA-TAA
847364 ACTATCGCAACG
1 ACTATCGCAACG
847376 AGATAATCGC
Statistics
Matches: 140, Mismatches: 19, Indels: 41
0.70 0.09 0.20
Matches are distributed among these distances:
14 16 0.11
15 5 0.04
16 1 0.01
17 1 0.01
18 3 0.02
19 22 0.16
20 88 0.63
21 2 0.01
22 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (19 bp):
ACTATCGCAACGCGAATAA
Found at i:847274 original size:54 final size:54
Alignment explanation
Indices: 847199--847355 Score: 235
Period size: 54 Copynumber: 2.9 Consensus size: 54
847189 CGAATAGACT
* * * * *
847199 ATCGCAACGCGAATATAACTATTGCAACGTGAATTTGAATATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGAATATCGCAACGGGATA
* *
847253 ATCGCAATGCGAAAATGACTATCACAACGCGAATTTGACTATCGCAACGGGATA
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGAATATCGCAACGGGATA
847307 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTT-AACTATCGCAACG
1 ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGAA-TATCGCAACG
847356 CGAATTTGAC
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.01
54 92 0.99
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (54 bp):
ATCGCAATGCGAAAATGACTATCGCAACGCGAATTTGAATATCGCAACGGGATA
Found at i:847326 original size:34 final size:34
Alignment explanation
Indices: 847288--847408 Score: 127
Period size: 40 Copynumber: 3.4 Consensus size: 34
847278 AACGCGAATT
847288 TGACTATCGCAACGGGATAATCGCAATGCGAAAA
1 TGACTATCGCAACGGGATAATCGCAATGCGAAAA
* * **
847322 TGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATT
1 TGACTATCGCAACG-GGA--T-A--ATCGCAATGCGAAAA
*
847362 TGACTATCGCAACGAGATAATCGCAATGCG-AAA
1 TGACTATCGCAACGGGATAATCGCAATGCGAAAA
*
847395 TGATTATCGCAACG
1 TGACTATCGCAACG
847409 CGAATTTGAT
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
33 14 0.20
34 24 0.34
35 2 0.03
36 1 0.01
37 2 0.03
38 1 0.01
39 1 0.01
40 26 0.37
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (34 bp):
TGACTATCGCAACGGGATAATCGCAATGCGAAAA
Found at i:847331 original size:74 final size:73
Alignment explanation
Indices: 847175--847487 Score: 301
Period size: 74 Copynumber: 4.3 Consensus size: 73
847165 CACATTCATT
* * * * * * *
847175 TGACTATCGCAACGCGAA-TAGACTATCGCAACGCGAATATAACTATTGCAACGTGA-ATTTG-A
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCA
* *
847237 ATATCGCAACG
66 AT-GCG-AA-A
* * ** * *
847248 GGA-TAATCGCAATGCGAAAATGACTATCACAACGCGAATTTGACTATCGCAACGGGATAATCGC
1 TGACT-ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGC
847312 AATGCGAAAA
65 AATGCG-AAA
*
847322 TGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCA
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCA
847387 ATGCGAAA
66 ATGCGAAA
* * * * * * *
847395 TGATTATCGCAACGCGAATTTGATTATCGCAACGGGAATTTAACTATCGCAATGAGAAAATCGTA
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCA
* * * *
847460 AAGTGTAT
66 ATGCGAAA
847468 TAGACTATCGCAACGCGAAT
1 T-GACTATCGCAACGCGAAT
847488 ATGATGCAGA
Statistics
Matches: 200, Mismatches: 34, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
72 1 0.00
73 79 0.40
74 109 0.55
75 8 0.04
76 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (73 bp):
TGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCGCAACGAGATAATCGCA
ATGCGAAA
Found at i:847420 original size:20 final size:20
Alignment explanation
Indices: 847381--847446 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
847371 CAACGAGATA
* * *
847381 ATCGCAATGCGAA-ATGATT
1 ATCGCAACGCGAATTTGACT
*
847400 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
847420 ATCGCAACGGGAATTTAACT
1 ATCGCAACGCGAATTTGACT
847440 ATCGCAA
1 ATCGCAA
847447 TGAGAAAATC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:847627 original size:28 final size:29
Alignment explanation
Indices: 847595--847655 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
847585 ATTAACAAGC
*
847595 ACAAATAAGAAATATT-TACATCAATTAA
1 ACAAATAAGAAATATTACACATCAATTAA
*
847623 ACAAATAAGAATTATTACACATCAATTAA
1 ACAAATAAGAAATATTACACATCAATTAA
847652 ACAA
1 ACAA
847656 TCAACTCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.57, C:0.13, G:0.03, T:0.26
Consensus pattern (29 bp):
ACAAATAAGAAATATTACACATCAATTAA
Found at i:849624 original size:20 final size:20
Alignment explanation
Indices: 849599--849684 Score: 91
Period size: 20 Copynumber: 4.3 Consensus size: 20
849589 AATAGTTTCT
*
849599 GAAACTTAAAATCGTAACAC
1 GAAACTTAAAATCGCAACAC
849619 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
* * ** *
849639 GAAAATGATTATCGCAACGC
1 GAAACTTAAAATCGCAACAC
** *
849659 GAAACCAAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
849679 GAAACT
1 GAAACT
849685 AAATTCGCGT
Statistics
Matches: 54, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.48, C:0.23, G:0.14, T:0.15
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:849752 original size:20 final size:20
Alignment explanation
Indices: 849727--849846 Score: 119
Period size: 20 Copynumber: 6.3 Consensus size: 20
849717 GCAATTATCC
849727 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
849747 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAAATT-CG
* ***
849767 CGTTGTGATAGTCGTTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
849787 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
849801 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
849821 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
849841 CGTTGC
1 CGTTGC
849847 TATAATCATT
Statistics
Matches: 83, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.12
16 1 0.01
18 1 0.01
19 4 0.05
20 64 0.77
21 3 0.04
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:849821 original size:34 final size:34
Alignment explanation
Indices: 849692--849829 Score: 132
Period size: 34 Copynumber: 3.9 Consensus size: 34
849682 ACTAAATTCG
** *
849692 CGTTGCGATAGTCATTTTTCGCATTGCAATTATCC
1 CGTTGCGATAGTCA-AATTCGCATTGCGATTATCC
*
849727 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTCC
1 CGTTGCGATAGTCAAATTCGCATTGCGAT--T-A--TCC
* ***
849766 GCGTTGTGATAGTCGTTTTCGCATTGCGATTATCC
1 -CGTTGCGATAGTCAAATTCGCATTGCGATTATCC
*
849801 CGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCATTGCGAT
849830 AGTCAAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 13
0.75 0.13 0.12
Matches are distributed among these distances:
34 35 0.42
35 17 0.20
36 1 0.01
37 2 0.02
38 1 0.01
39 3 0.04
40 24 0.29
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCATTGCGATTATCC
Found at i:849860 original size:20 final size:20
Alignment explanation
Indices: 849801--849868 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
849791 GCGATTATCC
*
849801 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
*
849821 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAATCAAATTCG
* **
849841 CGTTGCTATAATCATTTTCG
1 CGTTGCGATAATCAAATTCG
*
849861 TGTTGCGA
1 CGTTGCGA
849869 CTATTCTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAATCAAATTCG
Found at i:849868 original size:74 final size:74
Alignment explanation
Indices: 849685--849860 Score: 266
Period size: 74 Copynumber: 2.4 Consensus size: 74
849675 ACGCGAAACT
* *
849685 AAATTCGCGTTGCGATAGTCATTTTTCGCATTGCAATTATCCCGTTGCGATAGTCAAATTCGCGT
1 AAATTCGCGTTGCTATAGTCA-TTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGT
849750 TGCGATAGTC
65 TGCGATAGTC
* *
849760 -ATTTCCGCGTTG-TGATAGTCGTTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCG
1 AAATT-CGCGTTGCT-ATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCG
849823 TTGCGATAGTC
64 TTGCGATAGTC
*
849834 AAATTCGCGTTGCTATAATCATTTTCG
1 AAATTCGCGTTGCTATAGTCATTTTCG
849861 TGTTGCGACT
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
74 73 0.81
75 17 0.19
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (74 bp):
AAATTCGCGTTGCTATAGTCATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAATTCGCGTT
GCGATAGTC
Found at i:850046 original size:32 final size:31
Alignment explanation
Indices: 849987--850048 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
849977 CTACTACCGA
849987 ATGAATTTACTAAGCAATCCAAAAGACAAAT
1 ATGAATTTACTAAGCAATCCAAAAGACAAAT
*
850018 ATGAATTTACTAACTTCAA-CCAAAAGACAAA
1 ATGAATTTACTAA--GCAATCCAAAAGACAAA
850049 ACAAAGACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.52, C:0.18, G:0.08, T:0.23
Consensus pattern (31 bp):
ATGAATTTACTAAGCAATCCAAAAGACAAAT
Found at i:851863 original size:20 final size:20
Alignment explanation
Indices: 851840--851895 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
851830 TCTGAAACTT
851840 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
*
851860 AAAATCGCAGCACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
851880 ATTATCGCAACGCGAA
1 AAAATCGCAACACGAA
851896 TTTGACTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:851905 original size:20 final size:20
Alignment explanation
Indices: 851882--851937 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
851872 CGAAAATGAT
851882 TATCGCAACGCGAATTTGAC
1 TATCGCAACGCGAATTTGAC
* *
851902 TATCGCAACGCGAA-ATGGC
1 TATCGCAACGCGAATTTGAC
* *
851921 TATCACAACGAGAATTT
1 TATCGCAACGCGAATTT
851938 TGTCGTTGCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
TATCGCAACGCGAATTTGAC
Found at i:851929 original size:19 final size:20
Alignment explanation
Indices: 851843--851935 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
851833 GAAACTTAAA
* * **
851843 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAATATGACT
* * * *
851863 ATCGCAGCACGAAAATGATT
1 ATCGCAACGCGAATATGACT
*
851883 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
*
851903 ATCGCAACGCGAA-ATGGCT
1 ATCGCAACGCGAATATGACT
* *
851922 ATCACAACGAGAAT
1 ATCGCAACGCGAAT
851936 TTTGTCGTTG
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.25
20 45 0.75
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:852285 original size:22 final size:22
Alignment explanation
Indices: 852258--852330 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
852248 GATGGAGATA
852258 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* * *
852280 GACGGATTTCGCCGTAAATGAG
1 GACGGATTTCGCCGGAGATGGG
*
852302 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
852324 GACGGAT
1 GACGGAT
852331 GTTTCCGTAG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.22, C:0.16, G:0.41, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:852545 original size:41 final size:41
Alignment explanation
Indices: 852500--852586 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
852490 TTATCGCAAC
* * * *
852500 GCGATAGTCAGAATCTCGTTGCGATCACGTATTATCGCGTT
1 GCGATAGTCAGAATCGCGCTGCGATCAAGCATTATCGCGTT
* * *
852541 GCGATAGTCCGGATCGCGCTGCGATCAAGCGTTATCGCGTT
1 GCGATAGTCAGAATCGCGCTGCGATCAAGCATTATCGCGTT
852582 GCGAT
1 GCGAT
852587 TTACATATTC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.28
Consensus pattern (41 bp):
GCGATAGTCAGAATCGCGCTGCGATCAAGCATTATCGCGTT
Found at i:852603 original size:20 final size:20
Alignment explanation
Indices: 852575--852627 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
852565 TCAAGCGTTA
*
852575 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
852595 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
852615 TCGCATTGCGATT
1 TCGCATTGCGATT
852628 ATCTAAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:852725 original size:20 final size:19
Alignment explanation
Indices: 852701--852747 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
852691 TGAAAACTGA
*
852701 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
852721 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
852740 ATTGCGAT
1 ATTGCGAT
852748 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:852737 original size:19 final size:19
Alignment explanation
Indices: 852713--852749 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
852703 TGCGATAATG
*
852713 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
852732 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
852750 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:852931 original size:21 final size:21
Alignment explanation
Indices: 852907--852952 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
852897 GATTAGTGAT
852907 ACTAAACAAAATTAAATTCCA
1 ACTAAACAAAATTAAATTCCA
*
852928 ACTAAAGAAAATTAAATTCCA
1 ACTAAACAAAATTAAATTCCA
852949 ACTA
1 ACTA
852953 TTTAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (21 bp):
ACTAAACAAAATTAAATTCCA
Found at i:855343 original size:10 final size:12
Alignment explanation
Indices: 855312--855343 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
855302 AATGGTTTGA
855312 AGTGATTATAAG
1 AGTGATTATAAG
855324 AGTGATTATAAG
1 AGTGATTATAAG
855336 -GT-ATTATA
1 AGTGATTATA
855344 TGTTCAGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 6 0.30
11 2 0.10
12 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (12 bp):
AGTGATTATAAG
Found at i:857955 original size:17 final size:17
Alignment explanation
Indices: 857906--857956 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
857896 TTTTTAAAAA
*
857906 TATAATTTTTAATTATT
1 TATAATTTTAAATTATT
**
857923 TA-ACA-TTTCGATTATT
1 TATA-ATTTTAAATTATT
857939 TATAATTTTAAATTATT
1 TATAATTTTAAATTATT
857956 T
1 T
857957 TACGTATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
TATAATTTTAAATTATT
Found at i:859879 original size:16 final size:18
Alignment explanation
Indices: 859853--859889 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
859843 TAATTCAAAC
*
859853 AAATAATTTTT-AATTTA
1 AAATAATTTTTCAATTCA
859870 AAAT-ATTTTTCAATTCA
1 AAATAATTTTTCAATTCA
859887 AAA
1 AAA
859890 GTTTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
AAATAATTTTTCAATTCA
Found at i:867573 original size:21 final size:21
Alignment explanation
Indices: 867549--867624 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
867539 TCGTACCAAG
*
867549 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
* * *
867570 GACGAGGATATCATTCATCAA
1 GACGAGAAGACCATTCATCAA
867591 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
867612 GACGAGAAGACCA
1 GACGAGAAGACCA
867625 CATCGCATGG
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 1 0.02
21 46 0.98
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:870235 original size:17 final size:16
Alignment explanation
Indices: 870215--870260 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
870205 AGAGAAATGT
*
870215 AGAAAGAGAAAAGGAAA
1 AGAAA-AGAAAAAGAAA
870232 AGAAAAGAATAAAGAAA
1 AGAAAAGAA-AAAGAAA
870249 AGAAAAGAAAAA
1 AGAAAAGAAAAA
870261 ATTGAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (16 bp):
AGAAAAGAAAAAGAAA
Found at i:870238 original size:5 final size:5
Alignment explanation
Indices: 870215--870259 Score: 54
Period size: 5 Copynumber: 8.2 Consensus size: 5
870205 AGAGAAATGT
870215 AGAAA GAGAAA AGGAAA AGAAA AGAATAA AGAAA AGAAA AGAAA A
1 AGAAA -AGAAA A-GAAA AGAAA AG-A-AA AGAAA AGAAA AGAAA A
870260 AATTGAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 20 0.56
6 12 0.33
7 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (5 bp):
AGAAA
Found at i:870245 original size:12 final size:11
Alignment explanation
Indices: 870215--870259 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
870205 AGAGAAATGT
*
870215 AGAAAGAGAAA
1 AGAAAAAGAAA
*
870226 AGGAAAAGAAA
1 AGAAAAAGAAA
870237 AGAATAAAGAAA
1 AGAA-AAAGAAA
870249 AG-AAAAGAAA
1 AGAAAAAGAAA
870259 A
1 A
870260 AATTGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 8 0.27
11 13 0.43
12 9 0.30
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:873242 original size:55 final size:55
Alignment explanation
Indices: 873158--874063 Score: 1360
Period size: 55 Copynumber: 16.6 Consensus size: 55
873148 TGAAGCAAAA
* *
873158 GAAGATTGTTTGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
873213 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
873268 GAAGATT-AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
873321 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
873376 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
873429 GAAGATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCATACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * * *
873482 GAAGATTGTTTGGGTTTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
873537 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
873592 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCATACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * **
873647 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAACAGGGGGGCAGACACGATTTTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGGGCAGACGCGATCGTT
* *
873703 GAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCGGACGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
873758 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGTAGACGCGATCGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
873813 GAAGATTGTTCGAGTCTTATACTTTCTGAAGAAATAGGGGGCAGACGCGATCAG-T
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATC-GTT
* * *
873868 GAAGATTGTTCGAGTCTTATACTCTTTGAAGAAATAGGGGGCAGATGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * * *
873923 AAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGTGAGCAGACACGAAT-GTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCG-ATCGTT
* * * ** *
873978 GAAAATTGTTCGAGTCTAATACTCTCTGAAGAAATAGGGAGCAGAAACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
874033 GAAGATTGTTCGAGTCTTATACTCTCTGAAG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAG
874064 CATAGAGATC
Statistics
Matches: 783, Mismatches: 59, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
53 148 0.19
54 7 0.01
55 574 0.73
56 54 0.07
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.29
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:883383 original size:2 final size:2
Alignment explanation
Indices: 883376--883404 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
883366 CCTCTCAGAC
883376 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
883405 ATTTAAGCCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:885096 original size:11 final size:11
Alignment explanation
Indices: 885082--885144 Score: 60
Period size: 11 Copynumber: 5.8 Consensus size: 11
885072 AAACATAAGG
*
885082 GAAATAAATAT
1 GAAATAAAAAT
885093 GAAATAAAAAT
1 GAAATAAAAAT
885104 GAAAT-AAAAT
1 GAAATAAAAAT
885114 -ATAATAAAAA-
1 GA-AATAAAAAT
* *
885124 CAACATACAAAT
1 GAA-ATAAAAAT
885136 GAAATAAAA
1 GAAATAAAA
885145 TAAAAAAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 1 0.02
10 9 0.21
11 31 0.72
12 2 0.05
ACGTcount: A:0.70, C:0.05, G:0.06, T:0.19
Consensus pattern (11 bp):
GAAATAAAAAT
Found at i:885161 original size:31 final size:32
Alignment explanation
Indices: 885100--885163 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
885090 TATGAAATAA
885100 AAATGAAATAAAATATAATAAAAACAACATAC
1 AAATGAAATAAAATATAATAAAAACAACATAC
885132 AAATGAAATAAAATA-AA-AAAACACAACATAC
1 AAATGAAATAAAATATAATAAAA-ACAACATAC
885163 A
1 A
885164 TTTATACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 4 0.13
31 12 0.39
32 15 0.48
ACGTcount: A:0.70, C:0.11, G:0.03, T:0.16
Consensus pattern (32 bp):
AAATGAAATAAAATATAATAAAAACAACATAC
Found at i:885927 original size:101 final size:101
Alignment explanation
Indices: 885812--886013 Score: 368
Period size: 101 Copynumber: 2.0 Consensus size: 101
885802 ATTAGCAAAT
*
885812 TAAGTGGATGAATTCGAATATCAACAAAAATAAACAACACATGTAATAAGTGACTAAAATAAAAT
1 TAAGTGGATGAATTCGAATATCAACAAAAATAAACAACACATATAATAAGTGACTAAAATAAAAT
* *
885877 ATTTAAAATTTTAATGTCCAAATTCATACATTCACG
66 ATTTAAAAATTTAATGTCCAAATTCAAACATTCACG
*
885913 TAAGTGGCTGAATTCGAATATCAACAAAAATAAACAACACATATAATAAGTGACTAAAATAAAAT
1 TAAGTGGATGAATTCGAATATCAACAAAAATAAACAACACATATAATAAGTGACTAAAATAAAAT
885978 ATTTAAAAATTTAATGTCCAAATTCAAACATTCACG
66 ATTTAAAAATTTAATGTCCAAATTCAAACATTCACG
886014 AAAATGATAA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 97 1.00
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (101 bp):
TAAGTGGATGAATTCGAATATCAACAAAAATAAACAACACATATAATAAGTGACTAAAATAAAAT
ATTTAAAAATTTAATGTCCAAATTCAAACATTCACG
Found at i:887267 original size:3 final size:3
Alignment explanation
Indices: 887259--887299 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
887249 ATAACAAATT
*
887259 TAA TAA TAA TAT TAA TTAA TTAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA TAA TAA
887300 AGACCCAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 28 0.80
4 7 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:887816 original size:133 final size:131
Alignment explanation
Indices: 887482--887841 Score: 488
Period size: 133 Copynumber: 2.7 Consensus size: 131
887472 AGTTCGGGTC
* * *
887482 ATCTAAGGGTGACACGGTTCGTACGTGATGAGGAAATCTGGTCGAGGGATGACACTGCTCATACG
1 ATCT-AGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACAC-GCTCATACG
** * *
887547 TGATGAAGAGTTCTTGGCCATCTTTAGGAAAGGTGATAACTCGGTTCCTACTCGATGAGGACGAC
63 TGATGAAGAGTTC-TGGCCATCTTTAGGAAAGGCAATAACACGGTTCCTACTCGATGAGAACGAC
887612 TGGTT
127 TGGTT
* * *
887617 ATCTAGGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGGGACGACACGGCTCATACG
1 ATCTA-GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-AGGGATGACAC-GCTCATACG
* * *
887682 TGATGAAGAGTTCTGGCCATCTTTAGGAAGGGCAATAACACGGTTCCTA-TGTGATGAGAACGTC
63 TGATGAAGAGTTCTGGCCATCTTTAGGAAAGGCAATAACACGGTTCCTACT-CGATGAGAACGAC
887746 TGGTT
127 TGGTT
* *
887751 ATCTAGGGTGACGCGGCTCCTACGTGATGAAGAGATCTGGTCAGGAGATGACACGACTCATACGT
1 ATCTAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGG-GATGACACG-CTCATACGT
887816 GATGAAGAGTTCTGGCCATCTTTAGG
64 GATGAAGAGTTCTGGCCATCTTTAGG
887842 GATAATAATT
Statistics
Matches: 202, Mismatches: 19, Indels: 10
0.87 0.08 0.04
Matches are distributed among these distances:
132 3 0.01
133 77 0.38
134 53 0.26
135 69 0.34
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (131 bp):
ATCTAGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGATGACACGCTCATACGTGA
TGAAGAGTTCTGGCCATCTTTAGGAAAGGCAATAACACGGTTCCTACTCGATGAGAACGACTGGT
T
Found at i:888138 original size:30 final size:29
Alignment explanation
Indices: 888104--888161 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
888094 ACAAAACTTT
888104 GTTTCAAAAGAAACAAACTCAAAGATTTTG
1 GTTTCAAAAGAAA-AAACTCAAAGATTTTG
* **
888134 GTTTCAAAATAAATGACTCAAAGATTTT
1 GTTTCAAAAGAAAAAACTCAAAGATTTT
888162 TTCACGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (29 bp):
GTTTCAAAAGAAAAAACTCAAAGATTTTG
Found at i:888201 original size:91 final size:91
Alignment explanation
Indices: 888056--888251 Score: 261
Period size: 91 Copynumber: 2.1 Consensus size: 91
888046 GAGACGGAAT
* * *
888056 CTCAAAGATTTTTCTCAAGAAAAACTGTCTCAAGATAGACAAAACTTTGTTTCAAAAGAAACAAA
1 CTCAAAGATTTTTCTCAAG-AAAACTGTCTCAAGAGAAACAAAACTTTGATTCAAAAGAAACAAA
* **
888121 CTCAAAGATTTTGGTTTCAAAATAAATGA
65 CTCAAAGATTTT--TTTCAAAAGAAACAA
* * * *
888150 CTCAAAGATTTTT-TCACG-AAATTGTCTTAAGAGAAACAAAACTTTGATTCAAAAGAAACAGAC
1 CTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGAGAAACAAAACTTTGATTCAAAAGAAACAAAC
888213 TCAAAGATTTTTTTCAAAAGAAACAA
66 TCAAAGATTTTTTTCAAAAGAAACAA
888239 CTCAAAGATTTTT
1 CTCAAAGATTTTT
888252 ATTTCAAAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
89 25 0.27
91 50 0.54
93 4 0.04
94 13 0.14
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (91 bp):
CTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGAGAAACAAAACTTTGATTCAAAAGAAACAAAC
TCAAAGATTTTTTTCAAAAGAAACAA
Found at i:888347 original size:30 final size:28
Alignment explanation
Indices: 888192--888356 Score: 152
Period size: 29 Copynumber: 5.6 Consensus size: 28
888182 GAAACAAAAC
* *
888192 TTTGATTCAAAAGAAACAGACTCAAAGAT
1 TTTGTTTCAAGAGAAACA-ACTCAAAGAT
*
888221 TTT-TTTCAAAAGAAACAACTCAAAGATT
1 TTTGTTTCAAGAGAAACAACTCAAAGA-T
* * *
888249 TTTATTTCAAAAGAAACAACTCACAGACT
1 TTTGTTTCAAGAGAAACAACTCAAAGA-T
888278 TTTGTTTCAAGAGAAACAAACTCAAAGATAGGT
1 TTTGTTTCAAGAGAAAC-AACTCAAAG--A--T
* *
888311 TTTGTTTCAAGGGAAACAATTTCAAAGAT
1 TTTGTTTCAAGAGAAACAA-CTCAAAGAT
*
888340 GTTTGTTTTAAGAGAAA
1 -TTTGTTTCAAGAGAAA
888357 TTGTCTTAAA
Statistics
Matches: 117, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
27 9 0.08
28 17 0.15
29 42 0.36
30 22 0.19
31 1 0.01
32 3 0.03
33 23 0.20
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (28 bp):
TTTGTTTCAAGAGAAACAACTCAAAGAT
Found at i:888501 original size:64 final size:64
Alignment explanation
Indices: 888352--888541 Score: 217
Period size: 66 Copynumber: 3.0 Consensus size: 64
888342 TTGTTTTAAG
* * ** * * *
888352 AGAAATTGTCTTAAAAGAGACAAACCTTTGTATTCATAAAAACAAACTTAAAGATTTTTCTTCAA
1 AGAAACTGTCTCAAAAGAGACAAAATTTTGTATTCAAAAAAACATACTCAAAGA-TTTT-TTCAA
888417 A
64 A
* *
888418 AGGAACTGTCTTAAAAGAGACAAAATTTTGT-TTCCAAAAAAACATACTCAAAGATTTTTTCAAA
1 AGAAACTGTCTCAAAAGAGACAAAATTTTGTATT-CAAAAAAACATACTCAAAGATTTTTTCAAA
* *
888482 AGAAACTTTCTCAAAAGAGACAAAAATTTT-TATT-AAAGAAA-ATACTCAAAGATTTTTTCA
1 AGAAACTGTCTCAAAAGAGAC-AAAATTTTGTATTCAAAAAAACATACTCAAAGATTTTTTCA
888542 TTTTGTTTTA
Statistics
Matches: 110, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
62 19 0.17
63 6 0.05
64 25 0.23
65 16 0.15
66 44 0.40
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (64 bp):
AGAAACTGTCTCAAAAGAGACAAAATTTTGTATTCAAAAAAACATACTCAAAGATTTTTTCAAA
Found at i:888660 original size:30 final size:31
Alignment explanation
Indices: 888606--888664 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
888596 GAGACAAAGT
888606 TTTGTTTAAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTAAAAAGAAATAGACTCAAAGATCC
*
888637 TTTGTTTCAAAAGAAAT-GACTCAAAGAT
1 TTTGTTTAAAAAGAAATAGACTCAAAGAT
888665 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTTTAAAAAGAAATAGACTCAAAGATCC
Found at i:888742 original size:36 final size:36
Alignment explanation
Indices: 888702--888797 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
888692 ATAATTTGGA
*
888702 AAATTGTCTCAAGTGAGACAACATTTATTTTCAGAG
1 AAATTGTCTCAAGTGAGACAACAATTATTTTCAGAG
** * * *
888738 AAATTGTCTCAAACGAGACAAAAATTGTTTTTAGAG
1 AAATTGTCTCAAGTGAGACAACAATTATTTTCAGAG
*
888774 AAATTGATATCAAGTGAGATCAAC
1 AAATTG-TCTCAAGTGAGA-CAAC
888798 TTTGTTTAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
36 36 0.75
37 9 0.19
38 3 0.06
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (36 bp):
AAATTGTCTCAAGTGAGACAACAATTATTTTCAGAG
Found at i:888944 original size:104 final size:104
Alignment explanation
Indices: 888742--889081 Score: 379
Period size: 105 Copynumber: 3.2 Consensus size: 104
888732 TCAGAGAAAT
* *** *
888742 TGTCTCAAACGAGACA-AAAATTGTTTT-TAGAGAAATTGATATCAAGTGAGATCAACTTTGTTT
1 TGTCTCAAACGAGA-AGAAATTTGTTTTATA-AGAAAGCAATCTCAAGTGAGATCAACTTTGTTT
888805 AATGTGAAACAAATTCAAAATTTGTATTCTCAAAGGAAAAA
64 AATGTGAAACAAATTCAAAATTTGTATTCTCAAAGGAAAAA
* * *
888846 TG-CTTCAAATGAGAAGAAATTTGTTTTGAATAA-AAA-CAATCTCAAGTGAGATTAATTTTTGT
1 TGTC-TCAAACGAGAAGAAATTTGTTTT--ATAAGAAAGCAATCTCAAGTGAGATCAA-CTTTGT
* *
888908 TTCAA-GTGAATCAAATTCAAAATTTGTA-TATCAAAGGAAAAAA
62 TT-AATGTGAAACAAATTCAAAATTTGTATTCTCAAAGG-AAAAA
* * * * * * *
888951 TGTCTCAAGCAAGACGAAGTTTGTTTTTTAAGAAAGCGATCTCAAATGAGATCAACTTTGTTTAA
1 TGTCTCAAACGAGAAGAAATTTGTTTTATAAGAAAGCAATCTCAAGTGAGATCAACTTTGTTTAA
*
889016 TGTGAAACAAATTCTAAATTTGTATTCTCAAAGGAAAAA
66 TGTGAAACAAATTCAAAATTTGTATTCTCAAAGGAAAAA
*
889055 TGTCTCAAACGAGAAAGAATTTTGTTT
1 TGTCTCAAACGAG-AAGAAATTTGTTT
889082 CTCAAATGTG
Statistics
Matches: 196, Mismatches: 26, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
103 7 0.04
104 91 0.46
105 92 0.47
106 4 0.02
107 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (104 bp):
TGTCTCAAACGAGAAGAAATTTGTTTTATAAGAAAGCAATCTCAAGTGAGATCAACTTTGTTTAA
TGTGAAACAAATTCAAAATTTGTATTCTCAAAGGAAAAA
Found at i:893205 original size:31 final size:31
Alignment explanation
Indices: 893144--893207 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 31
893134 TATTAAATAA
*
893144 AAATGAAATAAAATATTATAAAAACAACATAC
1 AAATGAAATAAAATA-TAAAAAAACAACATAC
893176 AAATGAAATAAAATA-AAAAAACACAACATAC
1 AAATGAAATAAAATATAAAAAA-ACAACATAC
893207 A
1 A
893208 TTTATACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 5 0.17
31 10 0.33
32 15 0.50
ACGTcount: A:0.69, C:0.11, G:0.03, T:0.17
Consensus pattern (31 bp):
AAATGAAATAAAATATAAAAAAACAACATAC
Found at i:901702 original size:41 final size:42
Alignment explanation
Indices: 901611--901724 Score: 117
Period size: 41 Copynumber: 2.7 Consensus size: 42
901601 ATTGTCCTTA
* * * *
901611 TTATATATTTATTTTTTTAACAATTT-GAATTCTACTATAAT
1 TTATATATATATTTTTTTAAAAATTTAAAATTCTACTAAAAT
* *
901652 TAATTTATATATTTTCTTTAAAAATTTAAAATTC-A-TAAAAT
1 TTATATATATATTTT-TTTAAAAATTTAAAATTCTACTAAAAT
*
901693 TTATATATATATTTTTTTTACAAAATTGAAAA
1 TTATATATATA-TTTTTTTA-AAAATTTAAAA
901725 GATAAATAGG
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 30 0.50
42 25 0.42
43 5 0.08
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (42 bp):
TTATATATATATTTTTTTAAAAATTTAAAATTCTACTAAAAT
Found at i:910532 original size:20 final size:19
Alignment explanation
Indices: 910507--910594 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 19
910497 TTGAATTTCA
910507 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTT-TG
*
910527 AATTCGCAACGCGAATTTTG
1 AATTCGCAACTCG-ATTTTG
**
910547 TTTTCGCAACTCGATTTTCG
1 AATTCGCAACTCGATTTT-G
*
910567 AATTCGCAACACGAATTTT-
1 AATTCGCAACTCG-ATTTTG
910586 AATTTCGCA
1 AA-TTCGCA
910595 CCAGGTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
19 7 0.12
20 41 0.72
21 9 0.16
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (19 bp):
AATTCGCAACTCGATTTTG
Found at i:910554 original size:40 final size:40
Alignment explanation
Indices: 910486--910594 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
910476 ACAGTTTCCA
* * *
910486 AATTCGCAACATTGAATTTCAAATTCGCAACTCGA-TTTCTG
1 AATTCGCAACA-CGAATTTTAATTTCGCAACTCGATTTTC-G
* **
910527 AATTCGCAACGCGAATTTTGTTTTCGCAACTCGATTTTCG
1 AATTCGCAACACGAATTTTAATTTCGCAACTCGATTTTCG
910567 AATTCGCAACACGAATTTTAATTTCGCA
1 AATTCGCAACACGAATTTTAATTTCGCA
910595 CCAGGTTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
40 44 0.76
41 14 0.24
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (40 bp):
AATTCGCAACACGAATTTTAATTTCGCAACTCGATTTTCG
Found at i:911545 original size:23 final size:23
Alignment explanation
Indices: 911519--911562 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
911509 ATTCGAAATT
911519 TGATCTTGGTCAATACCCGGACA
1 TGATCTTGGTCAATACCCGGACA
*
911542 TGATCTTGGTCAATACTCGGA
1 TGATCTTGGTCAATACCCGGA
911563 TTTTGATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (23 bp):
TGATCTTGGTCAATACCCGGACA
Found at i:914648 original size:205 final size:203
Alignment explanation
Indices: 914294--914686 Score: 632
Period size: 205 Copynumber: 1.9 Consensus size: 203
914284 TCCAAATGCA
*
914294 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAATAACACTTTCTAC
1 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
* *
914359 ACATCTAAAACCAACAAACAAAATTATTGAATTTTAGGTACTTAAACCAAACATTTTCAAACCAA
66 ACATCTAAAACCAACAAACAAAAATATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACCAA
*
914424 CAAGTATATAACAGTTAACAACACTTGCACAAACTTACAAATAACAACTGGTTGTTTATGCACAA
131 CAAGTATATAACAGTTAACAACACTTGCACAAAC-TACAAATAACAAATGG-TGTTTATGCACAA
914489 ATACATCAAT
194 ATACATCAAT
*
914499 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTTCTCAAACAACACTTTCTAC
1 TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
914564 ACATCTAAAACCAACAAACAACAAATA-TGAATTCTAGGTACTT-AACCAAACATTTTCAAACCA
66 ACATCTAAAACCAACAAACAA-AAATATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACCA
* * *
914627 ACAAAG-AGTATATA-TGTTAACAACACTTGCTCAAACTACCAATAACAAATGGTGTTTATG
130 AC-AAGTA-TATA-ACAGTTAACAACACTTGCACAAACTACAAATAACAAATGGTGTTTATG
914687 TACACTTTCA
Statistics
Matches: 176, Mismatches: 8, Indels: 10
0.91 0.04 0.05
Matches are distributed among these distances:
203 8 0.05
204 37 0.21
205 126 0.72
206 5 0.03
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (203 bp):
TTCACGCAGCTCACTTCAGGATTAACCTGCAGAAACCAAACATTTGCTCAAACAACACTTTCTAC
ACATCTAAAACCAACAAACAAAAATATTGAATTCTAGGTACTTAAACCAAACATTTTCAAACCAA
CAAGTATATAACAGTTAACAACACTTGCACAAACTACAAATAACAAATGGTGTTTATGCACAAAT
ACATCAAT
Found at i:915791 original size:21 final size:21
Alignment explanation
Indices: 915765--915881 Score: 146
Period size: 21 Copynumber: 5.6 Consensus size: 21
915755 GTGAATCGGG
* *
915765 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGGC
**
915786 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
915807 CTCTTGAACGGT-GGAGGGAC
1 CTCTTGAACGATGGGAGGGGC
*
915827 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
915848 CTCTTGAACGATAGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
915869 CTCTTGAATGATG
1 CTCTTGAACGATG
915882 ACATGTGAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
20 16 0.20
21 64 0.80
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:915832 original size:41 final size:42
Alignment explanation
Indices: 915765--915884 Score: 188
Period size: 41 Copynumber: 2.9 Consensus size: 42
915755 GTGAATCGGG
*
915765 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGGGGC
*
915807 CTCTTGAACGGT-GGAGGGACCTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGGGGC
* * *
915848 CTCTTGAACGATAGGAGGGGCCTCTTGAATGATGACA
1 CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACA
915885 TGTGAATCTG
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 39 0.54
42 33 0.46
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:916301 original size:21 final size:21
Alignment explanation
Indices: 916277--916324 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
916267 ACCATTGTCG
*
916277 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
* *
916298 TCACGCAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
916319 TCACGT
1 TCACGT
916325 GACTCCCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.15, T:0.19
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:916713 original size:40 final size:40
Alignment explanation
Indices: 916658--916736 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
916648 ACCTCCTAAT
* *
916658 AATATAAAAGCTCAAACATGGTTAAACGTCTACTAGTAAC
1 AATATAAAAGCTCAAACAAGGTTAAACGACTACTAGTAAC
916698 AATATAAAAGCTCAAACAAGGTTAAACGACTACTAGTAA
1 AATATAAAAGCTCAAACAAGGTTAAACGACTACTAGTAA
916737 TAACTTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.23
Consensus pattern (40 bp):
AATATAAAAGCTCAAACAAGGTTAAACGACTACTAGTAAC
Found at i:917939 original size:19 final size:19
Alignment explanation
Indices: 917890--917943 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
917880 AGTAGTTTCT
917890 GAAACTTAAAATCGCAACGC
1 GAAA-TTAAAATCGCAACGC
*
917910 GAAAATGAAAATCGCAACGC
1 G-AAATTAAAATCGCAACGC
917930 GAAATTAAAATCGC
1 GAAATTAAAATCGC
917944 GTTGCGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 12 0.39
20 16 0.52
21 3 0.10
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAATTAAAATCGCAACGC
Found at i:917975 original size:20 final size:20
Alignment explanation
Indices: 917950--918008 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
917940 TCGCGTTGCG
917950 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
*
917970 ATTTTCGTGTTGCAAATTTC
1 ATTTTCGTGTTGCGAATTTC
*
917990 ATTTTCATGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
918009 AAGTTTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.51
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:918375 original size:21 final size:21
Alignment explanation
Indices: 918349--918399 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
918339 AGATAGACGG
*
918349 ATTTCGCCGGAGATGAAACGA
1 ATTTCGCCGGAGACGAAACGA
918370 ATTTCGCCGGAGACGAAACGA
1 ATTTCGCCGGAGACGAAACGA
918391 ATTTCGCCG
1 ATTTCGCCG
918400 TAGAGAGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (21 bp):
ATTTCGCCGGAGACGAAACGA
Found at i:918525 original size:19 final size:20
Alignment explanation
Indices: 918503--918540 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
918493 AATATTGTGT
918503 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
918522 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
918541 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:919297 original size:6 final size:6
Alignment explanation
Indices: 919286--919310 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
919276 CCCTTAATTT
919286 CTCTTC CTCTTC CTCTTC CTCTTC C
1 CTCTTC CTCTTC CTCTTC CTCTTC C
919311 CGTACATTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CTCTTC
Found at i:921697 original size:33 final size:33
Alignment explanation
Indices: 921637--921699 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
921627 ATTCTGTTCT
*
921637 TTTATTTATAATTTTATTATTTATATTCTAAAC
1 TTTATTTAAAATTTTATTATTTATATTCTAAAC
921670 TTTATTTAAAATATTTATTATTT-TATTCTA
1 TTTATTTAAAAT-TTTATTATTTATATTCTA
921700 TTAAATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (33 bp):
TTTATTTAAAATTTTATTATTTATATTCTAAAC
Found at i:931157 original size:16 final size:16
Alignment explanation
Indices: 931138--931168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
931128 AAAATTGAAT
931138 AAAATAAAAACTTCAC
1 AAAATAAAAACTTCAC
*
931154 AAAATCAAAACTTCA
1 AAAATAAAAACTTCA
931169 TGCATGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAAAAACTTCAC
Found at i:937833 original size:34 final size:35
Alignment explanation
Indices: 937758--937837 Score: 92
Period size: 34 Copynumber: 2.3 Consensus size: 35
937748 AACAAACATC
* *
937758 TACCAAACTTTGAAAAATCATTTTAAATAAATATT
1 TACCAAACTTTGAAAAACCATTTTAAATAAATAAT
* *
937793 TACCAAACTTT-AAAAACCATTTTTCAA-AATTAAT
1 TACCAAACTTTGAAAAACCA-TTTTAAATAAATAAT
*
937827 TGCCAAACTTT
1 TACCAAACTTT
937838 TAACTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
34 22 0.56
35 17 0.44
ACGTcount: A:0.45, C:0.16, G:0.03, T:0.36
Consensus pattern (35 bp):
TACCAAACTTTGAAAAACCATTTTAAATAAATAAT
Found at i:939216 original size:12 final size:13
Alignment explanation
Indices: 939199--939232 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
939189 CTTAAATGAG
939199 AAGCTGAAACA-C
1 AAGCTGAAACAGC
939211 AAGCTGAAACAGTC
1 AAGCTGAAACAG-C
939225 AAGCTGAA
1 AAGCTGAA
939233 GTTCTCGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (13 bp):
AAGCTGAAACAGC
Found at i:940956 original size:16 final size:16
Alignment explanation
Indices: 940914--940959 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
940904 TGTGACCAAA
*
940914 ATACAATTTTATCATT
1 ATACAATTTTATAATT
940930 ATATCAA-TTTATAATT
1 ATA-CAATTTTATAATT
*
940946 TTACAATTTTATAA
1 ATACAATTTTATAA
940960 GGATTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
ATACAATTTTATAATT
Found at i:943179 original size:22 final size:24
Alignment explanation
Indices: 943147--943194 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
943137 TTTAGGAATT
*
943147 TAAATTTTTTAAAG-AAAA-TATA
1 TAAATTATTTAAAGTAAAATTATA
*
943169 TAAATTATTTATAGTAAAATTATA
1 TAAATTATTTAAAGTAAAATTATA
943193 TA
1 TA
943195 TTTTCATTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 4 0.18
24 6 0.27
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
TAAATTATTTAAAGTAAAATTATA
Found at i:962071 original size:28 final size:26
Alignment explanation
Indices: 962021--962087 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
962011 TATTTATAGA
* *
962021 TTTAAAAAAAATACATATATAAAAATGT
1 TTTAAAAAATATAAATATATAAAAA--T
962049 TTTAAAAAATATAAAT-TATTAAAAAT
1 TTTAAAAAATATAAATATA-TAAAAAT
*
962075 ATTAAAAAATATA
1 TTTAAAAAATATA
962088 TATAAAAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.37
27 2 0.06
28 20 0.57
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (26 bp):
TTTAAAAAATATAAATATATAAAAAT
Found at i:962461 original size:24 final size:24
Alignment explanation
Indices: 962426--962489 Score: 50
Period size: 24 Copynumber: 2.8 Consensus size: 24
962416 TTTGAAAGAT
962426 ATTTT-ATAATTTTATAATATT-TA
1 ATTTTAAT-ATTTTATAATATTATA
962449 ATATTTAATATTTTAT--T-TTA-A
1 AT-TTTAATATTTTATAATATTATA
962470 ATTTTAATAATTATTATAAT
1 ATTTTAAT-ATT-TTATAAT
962490 TTTAAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
20 6 0.18
21 8 0.24
22 5 0.15
23 2 0.06
24 11 0.32
25 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTTTAATATTTTATAATATTATA
Found at i:964895 original size:18 final size:18
Alignment explanation
Indices: 964863--964908 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
964853 ACCACGTCAG
964863 TATAATA-TA-TAATTA-
1 TATAATATTATTAATTAC
964878 TATTAATATTATTAATTAC
1 TA-TAATATTATTAATTAC
*
964897 TATATTATTATT
1 TATAATATTATT
964909 GTAACAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 5 0.19
17 2 0.08
18 15 0.58
19 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TATAATATTATTAATTAC
Found at i:968869 original size:12 final size:12
Alignment explanation
Indices: 968852--968891 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
968842 TAAATGTTAA
968852 ACGAACATGTTC
1 ACGAACATGTTC
**
968864 ACGAACAT-TAA
1 ACGAACATGTTC
968875 ACGAACATGTTC
1 ACGAACATGTTC
968887 ACGAA
1 ACGAA
968892 TGTTAAATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (12 bp):
ACGAACATGTTC
Found at i:968888 original size:57 final size:57
Alignment explanation
Indices: 968815--968948 Score: 187
Period size: 57 Copynumber: 2.4 Consensus size: 57
968805 TCGTGAACGC
* *
968815 TAAACGAATATATTCACGAATACTAAATAAATGTTAAACGAACATGTTCACGAACAT
1 TAAACGAACATGTTCACGAATACTAAATAAATGTTAAACGAACATGTTCACGAACAT
** * * * *
968872 TAAACGAACATGTTCACGAATGTTAAATGAGTGTTAAACGAATATGTTCATGAACAT
1 TAAACGAACATGTTCACGAATACTAAATAAATGTTAAACGAACATGTTCACGAACAT
*
968929 TAAACGAACACGTTCACGAA
1 TAAACGAACATGTTCACGAA
968949 CATTAAACGA
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 68 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (57 bp):
TAAACGAACATGTTCACGAATACTAAATAAATGTTAAACGAACATGTTCACGAACAT
Found at i:968897 original size:23 final size:23
Alignment explanation
Indices: 968844--968898 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
968834 ATACTAAATA
968844 AATGTTAAACGAACATGTTCACG
1 AATGTTAAACGAACATGTTCACG
**
968867 AACATTAAACGAACATGTTCACG
1 AATGTTAAACGAACATGTTCACG
968890 AATGTTAAA
1 AATGTTAAA
968899 TGAGTGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (23 bp):
AATGTTAAACGAACATGTTCACG
Found at i:968931 original size:23 final size:23
Alignment explanation
Indices: 968905--968977 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
968895 TAAATGAGTG
* * *
968905 TTAAACGAATATGTTCATGAACA
1 TTAAACGAACACGTTCACGAACA
968928 TTAAACGAACACGTTCACGAACA
1 TTAAACGAACACGTTCACGAACA
*
968951 TTAAACGAACACATTC-CGAACA
1 TTAAACGAACACGTTCACGAACA
968973 TTAAA
1 TTAAA
968978 TAAATGAACA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 11 0.24
23 35 0.76
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (23 bp):
TTAAACGAACACGTTCACGAACA
Found at i:969010 original size:31 final size:31
Alignment explanation
Indices: 968974--969033 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
968964 TTCCGAACAT
** *
968974 TAAATAAATGAACACGAATACATCTAAAATA
1 TAAATAAACAAACACGAATACAACTAAAATA
*
969005 TAAATAAACAAACACGAATATAACTAAAA
1 TAAATAAACAAACACGAATACAACTAAAA
969034 AATTAAACGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.05, T:0.20
Consensus pattern (31 bp):
TAAATAAACAAACACGAATACAACTAAAATA
Found at i:976561 original size:42 final size:42
Alignment explanation
Indices: 976501--976583 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
976491 ATCTGCTCCG
* *
976501 GCTTCTTCTCCTCTGGCTGCTACTCCAGTGAGTTCGGCACCT
1 GCTTCTTCTCCTCCGGCTGCTACTCCAGTGAGTTCGCCACCT
*
976543 GCTTCTTCTCCTCCGGCTGCTCCTCCAGTGAGTTCGCCACC
1 GCTTCTTCTCCTCCGGCTGCTACTCCAGTGAGTTCGCCACC
976584 GCCTCCGGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.08, C:0.40, G:0.20, T:0.31
Consensus pattern (42 bp):
GCTTCTTCTCCTCCGGCTGCTACTCCAGTGAGTTCGCCACCT
Found at i:989793 original size:5 final size:5
Alignment explanation
Indices: 989783--989870 Score: 130
Period size: 5 Copynumber: 18.0 Consensus size: 5
989773 TCTAAAAAAC
989783 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
989833 ATTAT ATTAT ATT-T ATT-T ATT-T -TTATT ATTATT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTA-T ATTA-T ATTAT
989871 TTAGGTCCCA
Statistics
Matches: 80, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
3 2 0.03
4 9 0.11
5 60 0.75
6 9 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
ATTAT
Found at i:989962 original size:33 final size:33
Alignment explanation
Indices: 989925--989987 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
989915 ATAAATCAAC
989925 GTATTTGAGTCCTATTAAAACACTAAAACCAAT
1 GTATTTGAGTCCTATTAAAACACTAAAACCAAT
* * *
989958 GTATTTGAGTCTTATTGAAGCACTAAAACC
1 GTATTTGAGTCCTATTAAAACACTAAAACC
989988 GAATCATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (33 bp):
GTATTTGAGTCCTATTAAAACACTAAAACCAAT
Found at i:990401 original size:35 final size:34
Alignment explanation
Indices: 990310--990424 Score: 90
Period size: 35 Copynumber: 3.3 Consensus size: 34
990300 ACTTTATGTA
* * * *
990310 TATTTTTTTCATTTTCTCCTAAATTTAATATTT-TT
1 TATTTTTTTCATATTCT-TTTAATAT-ATATTTATT
* * *
990345 TATTTCTTTTTACATTGTTTTATATATATATTTATT
1 TATTT-TTTTCATATTCTTTTA-ATATATATTTATT
990381 TATTTTTTTCATATTCTTTTAATAT-TATTATATT
1 TATTTTTTTCATATTCTTTTAATATATATT-TATT
*
990415 AATGTTTTTT
1 TAT-TTTTTT
990425 TTATTATTCT
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
33 4 0.06
34 10 0.16
35 32 0.50
36 18 0.28
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (34 bp):
TATTTTTTTCATATTCTTTTAATATATATTTATT
Found at i:994209 original size:110 final size:109
Alignment explanation
Indices: 993986--994514 Score: 791
Period size: 110 Copynumber: 4.9 Consensus size: 109
993976 TGATGGTAGT
* * * *
993986 AGCTCAACTTCATAGCGTAA-GGGCGGCTGACTGTCAACAAACAACTTTTCAATTTCATT-CAGT
1 AGCTCAACTTCACAGCG-AAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTAGAGT
* * *
994049 TAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGTCAACACA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
*
994094 AGCTCAACTTCACAGCGAAGGGGCGACGGACTGTCAACAAACAACTTTTCAGTTTCATTAAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATT-AGAGT
*
994159 CAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
994204 AGCTCAACTTCACAGTGAAGGGGCGACTGACTTTCAACAAACAACTTTTCAATTTCATTCAGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATT-AGAGT
994269 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* * *
994314 AGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAATAAACAACTTTTCAGTTTCATTCAGAGG
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATT-AGAGT
994379 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
65 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* *
994424 AGCTCAACTTCACAGCGAAGGGGTGACTGGCTGTCAACAAACAAC-TTTCTAGTTTC---AGAGT
1 AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTC-AGTTTCATTAGAGT
* * *
994485 CAATTTCAATTTCACGGCGAATGATATTGG
65 CAATTTCAACTTCACAGCGAAGGATATTGG
994515 CCTTGAAACA
Statistics
Matches: 388, Mismatches: 29, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
106 31 0.08
107 2 0.01
108 52 0.13
109 4 0.01
110 299 0.77
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (109 bp):
AGCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTAGAGTC
AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
Found at i:994858 original size:84 final size:84
Alignment explanation
Indices: 994632--995003 Score: 555
Period size: 85 Copynumber: 4.4 Consensus size: 84
994622 AAGGGAATTG
* * * * * *
994632 TGCCCACCAAAGACTTTCGAGTTCGACTACGCTCAGCTCAAAGACACAACATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
994697 TAAGTCGAGAAGGGTTATC
66 TAAGTCGAGAAGGGTTATC
* * *
994716 TGTCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAAT
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
994781 TTAAGTCGAGAAGGGTTATC
65 TTAAGTCGAGAAGGGTTATC
* * *
994801 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTTAGCTTCAAGGCACATCATTTGCAGCATAGCT
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
*
994866 TAAGTCGAGAAGGGCTATC
66 TAAGTCGAGAAGGGTTATC
* *
994885 TGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGCATATCATTTGCAGCATAAC
1 TGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAAC
*
994950 TTAAGTCGAGAAGTGTTATC
65 TTAAGTCGAGAAGGGTTATC
* * *
994970 TGCCAACCAAAGACTTTTGAGTTCGAGTACGCTC
1 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
995004 TGCAGCATAA
Statistics
Matches: 260, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
84 107 0.41
85 153 0.59
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
TGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACT
TAAGTCGAGAAGGGTTATC
Found at i:994916 original size:169 final size:169
Alignment explanation
Indices: 994632--995003 Score: 620
Period size: 169 Copynumber: 2.2 Consensus size: 169
994622 AAGGGAATTG
*
994632 TGCCCACCAAAGACTTTCGAGTTCGACTACGCTCAGCTCAAAGACACAACATTTGCAGCATAGCT
1 TGCCAACCAAAGACTTTCGAGTTCGACTACGCTCAGCTCAAAGACACAACATTTGCAGCATAGCT
* * *
994697 TAAGTCGAGAAGGGTTATCTGTCAACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
66 TAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGC
*
994762 ATATCATTTGCAGCATAATTTAAGTCGAGAAGGGTTATC
131 ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* * * *
994801 TGCCAACCAAAGACCTTCGAGTTCGACTACGCTTAGCTTC-AAGGCACATCATTTGCAGCATAGC
1 TGCCAACCAAAGACTTTCGAGTTCGACTACGCTCAGC-TCAAAGACACAACATTTGCAGCATAGC
994865 TTAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGG
65 TTAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGG
*
994930 CATATCATTTGCAGCATAACTTAAGTCGAGAAGTGTTATC
130 CATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
* *
994970 TGCCAACCAAAGACTTTTGAGTTCGAGTACGCTC
1 TGCCAACCAAAGACTTTCGAGTTCGACTACGCTC
995004 TGCAGCATAA
Statistics
Matches: 188, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
169 186 0.99
170 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (169 bp):
TGCCAACCAAAGACTTTCGAGTTCGACTACGCTCAGCTCAAAGACACAACATTTGCAGCATAGCT
TAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCTCAACTCCAAGGC
ATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATC
Found at i:995137 original size:145 final size:147
Alignment explanation
Indices: 994854--995140 Score: 341
Period size: 145 Copynumber: 1.9 Consensus size: 147
994844 GCACATCATT
* * * *
994854 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAAGACCTTCGAGTTCGACTACGCT
1 TGCAGCATAACTTAAGTCAAGAAGGGCTATCTG---ACCAAAAGACCCTCGAGTTCGACTACACT
* * * *
994919 CAACTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGTGTTATCTGCCAACCAAAGAC
63 CAACTCCAAGGCACATCATTTACAGCATAAATCAAGTCGAGAAGTGTTATCTGCCAACCAAAGAC
* *
994984 TTTTGAGTTCGAGTACGCTC
128 CTTCGAGTTCGAGTACGCTC
* *
995004 TGCAGCATAACTTAAGTCAAGAAGGGCTATCTG-CC-AAAGACCCTCGAGTTCGATTACACTCAG
1 TGCAGCATAACTTAAGTCAAGAAGGGCTATCTGACCAAAAGACCCTCGAGTTCGACTACACTCAA
* * * *
995067 CTTCAAGGGCACATCATTTACATCATAAATCAA-TGCTAGAA-TGGTTATCTGTC-ACCAAAGAC
66 CTCCAA-GGCACATCATTTACAGCATAAATCAAGT-CGAGAAGT-GTTATCTGCCAACCAAAGAC
995129 CTTCGAGTTCGA
128 CTTCGAGTTCGA
995141 TTCCATTCAG
Statistics
Matches: 118, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
145 50 0.42
146 37 0.31
150 31 0.26
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (147 bp):
TGCAGCATAACTTAAGTCAAGAAGGGCTATCTGACCAAAAGACCCTCGAGTTCGACTACACTCAA
CTCCAAGGCACATCATTTACAGCATAAATCAAGTCGAGAAGTGTTATCTGCCAACCAAAGACCTT
CGAGTTCGAGTACGCTC
Done.