Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009606.1 Hibiscus syriacus cultivar Beakdansim tig00116990_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: 66290
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2869 original size:59 final size:60
Alignment explanation
Indices: 2806--2958 Score: 191
Period size: 59 Copynumber: 2.6 Consensus size: 60
2796 GATGAATTTG
* * * * *
2806 AGGATGAAATTGGAAGGTTTAAAAGTTTATGGACTAAAATAGAATAAG-GTGATAGCTTA
1 AGGATGAAATTAGAAGGTTTAAAAGTTCAAGGACTAAAATAGAATAAGTATCATAGCTTA
* ** *
2865 AGGATGAAATTAGAATGTTTAAAAGTTCAAGGACTAATTTAGAATAAGTATCATAGTTTA
1 AGGATGAAATTAGAAGGTTTAAAAGTTCAAGGACTAAAATAGAATAAGTATCATAGCTTA
* **
2925 AGGATGAAATTAAAATATTTAAAAGTTCAAGGAC
1 AGGATGAAATTAGAAGGTTTAAAAGTTCAAGGAC
2959 CAATTTAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 42 0.51
60 40 0.49
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (60 bp):
AGGATGAAATTAGAAGGTTTAAAAGTTCAAGGACTAAAATAGAATAAGTATCATAGCTTA
Found at i:2896 original size:29 final size:29
Alignment explanation
Indices: 2864--2957 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
2854 GTGATAGCTT
2864 AAGGATGAAATTAGAATGTTTAAAAGTTC
1 AAGGATGAAATTAGAATGTTTAAAAGTTC
* * * * *
2893 AAGGACT-AATTTAGAATAAGTATCATAGTTT
1 AAGGA-TGAAATTAGAAT--GTTTAAAAGTTC
* *
2924 AAGGATGAAATTAAAATATTTAAAAGTTC
1 AAGGATGAAATTAGAATGTTTAAAAGTTC
2953 AAGGA
1 AAGGA
2958 CCAATTTAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
29 26 0.53
30 2 0.04
31 21 0.43
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (29 bp):
AAGGATGAAATTAGAATGTTTAAAAGTTC
Found at i:2950 original size:60 final size:59
Alignment explanation
Indices: 2823--2983 Score: 196
Period size: 60 Copynumber: 2.7 Consensus size: 59
2813 AATTGGAAGG
* * ** * * * * *
2823 TTTAAAAGTTTATGGACTAAAATAGAATAAGGTGATAGCTTAAGGATGAAATTAGAATG
1 TTTAAAAGTTCAAGGACTAATTTAGAATAAGATCATAGTTTAAGGATGAAATTAAAATA
2882 TTTAAAAGTTCAAGGACTAATTTAGAATAAGTATCATAGTTTAAGGATGAAATTAAAATA
1 TTTAAAAGTTCAAGGACTAATTTAGAATAAG-ATCATAGTTTAAGGATGAAATTAAAATA
* * *
2942 TTTAAAAGTTCAAGGACCAATTTAAAAAGAAGATCATAGTTT
1 TTTAAAAGTTCAAGGACTAATTT-AGAATAAGATCATAGTTT
2984 GGGGACATAT
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
59 27 0.31
60 55 0.62
61 6 0.07
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (59 bp):
TTTAAAAGTTCAAGGACTAATTTAGAATAAGATCATAGTTTAAGGATGAAATTAAAATA
Found at i:2966 original size:29 final size:31
Alignment explanation
Indices: 2881--2968 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 31
2871 AAATTAGAAT
* *
2881 GTTTAAAAGTTCAAGGACTAATTTAGAATAA
1 GTTTAAAAGTTCAAGGACCAATTTAAAATAA
* * * * ** *
2912 GTATCATAGTTTAAGGATGAAATTAAAAT-A
1 GTTTAAAAGTTCAAGGACCAATTTAAAATAA
2942 -TTTAAAAGTTCAAGGACCAATTTAAAA
1 GTTTAAAAGTTCAAGGACCAATTTAAAA
2969 AGAAGATCAT
Statistics
Matches: 42, Mismatches: 15, Indels: 2
0.71 0.25 0.03
Matches are distributed among these distances:
29 20 0.48
30 1 0.02
31 21 0.50
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.32
Consensus pattern (31 bp):
GTTTAAAAGTTCAAGGACCAATTTAAAATAA
Found at i:14093 original size:17 final size:17
Alignment explanation
Indices: 14043--14093 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
14033 TTGCATTCCT
14043 TCTCTTTTTCTTCA-CA
1 TCTCTTTTTCTTCATCA
* * *
14059 T-TGCTTTGTATTCTTCA
1 TCT-CTTTTTCTTCATCA
14076 TCTCTTTTTCTTCATCA
1 TCTCTTTTTCTTCATCA
14093 T
1 T
14094 TTTCCTTTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 1 0.04
16 9 0.35
17 15 0.58
18 1 0.04
ACGTcount: A:0.12, C:0.25, G:0.04, T:0.59
Consensus pattern (17 bp):
TCTCTTTTTCTTCATCA
Found at i:14916 original size:18 final size:20
Alignment explanation
Indices: 14893--14941 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
14883 GCCATTTTTA
*
14893 TATCGATACTCATG-T-GAG
1 TATCGATACTCAGGATAGAG
*
14911 TATCGATACCCAGGATAGAG
1 TATCGATACTCAGGATAGAG
14931 TATCGATACTC
1 TATCGATACTC
14942 CCCGTAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 12 0.46
19 1 0.04
20 13 0.50
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
TATCGATACTCAGGATAGAG
Found at i:31008 original size:46 final size:46
Alignment explanation
Indices: 30941--31067 Score: 157
Period size: 45 Copynumber: 2.8 Consensus size: 46
30931 TAATATACCA
* ** * *
30941 TTATGTATTTTCATTGGTGGCATCCTTTCTTGCCAATTACGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAACGCACCG
* * * *
30987 TTATGCATTTTCATTTATGGCATCCTTT-ATGCCTATAATGTACTG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAACGCACCG
*
31032 TTATTCATTTTCATTTATGGCATCCTTTCATGCCAA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCAA
31068 AGGCATTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
45 38 0.55
46 31 0.45
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.45
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCAATAACGCACCG
Found at i:31200 original size:81 final size:81
Alignment explanation
Indices: 31065--32034 Score: 1422
Period size: 81 Copynumber: 12.0 Consensus size: 81
31055 CCTTTCATGC
* * * * *
31065 CAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGACACCTTTCTATCAAATGCACAGTTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
*
31130 CAATTAAACTTTTACT
66 CAATTAATCTTTTACT
* * *
31146 CAAAGGTATTTAACCTTTCATCTAATTGGCAGGATTGACACCTTTCTGTCAAATGCACATCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
*
31211 CAATTAGTCTTTTACT
66 CAATTAATCTTTTACT
* * *
31227 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGCATAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
*
31292 AAATTAATCTTTTACT
66 CAATTAATCTTTTACT
* * * * **
31308 CTAGGGTATTTAACCTTTCATCTAACTGACATGATTGACACCTTTTTGTCAAATGCACATATAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
* *
31373 CAACTAGTCTTTTACT
66 CAATTAATCTTTTACT
* * * * *
31389 TAAAGGTATTTAACCTTTCATCTAACTAGAATGATTGTCACATTTCTGTCAAATGCACAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
31454 CAATTAATCTTTTACT
66 CAATTAATCTTTTACT
* *
31470 CAAAGGTATTTAACCTTTCACCTAACTGACATGATTGACACCTTTCTGTCAAATGCACAAG-TAG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCAC-AGCTAG
31534 GCAATTAATCTTTTACT
65 GCAATTAATCTTTTACT
* * *
31551 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTTTGTCAAATGCACAACTAGA
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
31616 CAATTAATCTTTTACT
66 CAATTAATCTTTTACT
* *
31632 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGAAACCTTTCTGTCAAATGCACAGCTAGA
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
* * *
31697 CAAGTAGTCTTCTACT
66 CAATTAATCTTTTACT
* * * * *
31713 CAAATGTATTTAACCTTTCATCTAACAGGCATGATTTACACCTTTCTGTCAAATGCACACCTAGA
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
31778 CAATTAATCTTTTACT
66 CAATTAATCTTTTACT
* * * *
31794 AAAAGGTATTTAATCTTTCATCTAACTGGAATGATTGGA-ACCTTTATGTCAAATGCACAGCTAG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATT-GACACCTTTCTGTCAAATGCACAGCTAG
*
31858 ACAATTAATCTTTTACT
65 GCAATTAATCTTTTACT
* * * *
31875 CAAAGGTATTTAACATTTCATCTGACTGGCATGATTGACACCTTTCTTTCAAATGCACTGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
31940 CAATTAATCTTTTACT
66 CAATTAATCTTTTACT
* *
31956 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGT
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
*
32021 CAATTAGTCTTTTA
66 CAATTAATCTTTTA
32035 AAAACAGTTT
Statistics
Matches: 794, Mismatches: 91, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
80 3 0.00
81 788 0.99
82 3 0.00
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (81 bp):
CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
CAATTAATCTTTTACT
Found at i:32575 original size:94 final size:95
Alignment explanation
Indices: 32434--32618 Score: 252
Period size: 94 Copynumber: 2.0 Consensus size: 95
32424 CCCTACCATG
* **
32434 GTATTGATACTTCTACAATGTGGTATTGATAATTCCTTGCAGTATCGATACAATTTCT-ACATTC
1 GTATTGATACTTCTACAATATGGTACCGATAATTCCTTGCAGTATCGATACAATTT-TGACATTC
32498 TGG-ATCCATGGTATCGATACTTTCCTCCTA
65 TGGAATCCATGGTATCGATACTTTCCTCCTA
* * * *
32528 GTATTGATACTTCTATACTATGGTACCGAT-ATTCCCATT-CAGTATCGATACCATTTTGGCATT
1 GTATTGATACTTCTACAATATGGTACCGATAATT-CC-TTGCAGTATCGATACAATTTTGACATT
32591 CTGGAATCCATGGTATCGATACTTTCCT
64 CTGGAATCCATGGTATCGATACTTTCCT
32619 TTTTGGTATC
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
93 4 0.05
94 51 0.64
95 25 0.31
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (95 bp):
GTATTGATACTTCTACAATATGGTACCGATAATTCCTTGCAGTATCGATACAATTTTGACATTCT
GGAATCCATGGTATCGATACTTTCCTCCTA
Found at i:32646 original size:17 final size:17
Alignment explanation
Indices: 32624--32667 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
32614 TTCCTTTTTG
32624 GTATCGATACCCTATAA
1 GTATCGATACCCTATAA
*
32641 GTATCGATACCCTGTAA
1 GTATCGATACCCTATAA
32658 GTATCGATAC
1 GTATCGATAC
32668 TAATTGCATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (17 bp):
GTATCGATACCCTATAA
Found at i:33424 original size:9 final size:9
Alignment explanation
Indices: 33406--33449 Score: 79
Period size: 9 Copynumber: 4.9 Consensus size: 9
33396 ATCCTTTATC
*
33406 ATTTATTCA
1 ATTTAATCA
33415 ATTTAATCA
1 ATTTAATCA
33424 ATTTAATCA
1 ATTTAATCA
33433 ATTTAATCA
1 ATTTAATCA
33442 ATTTAATC
1 ATTTAATC
33450 CTCCAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTTAATCA
Found at i:37495 original size:46 final size:45
Alignment explanation
Indices: 37442--37570 Score: 143
Period size: 46 Copynumber: 2.8 Consensus size: 45
37432 ACCATTATAT
** *
37442 ATTTTCATTGGTGGCATTCTTTCATGCCAATTATGCATTGTCATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCAA-TATGCATTGTCATGC
* * * * * *
37488 ATTTTCATTTATGACATCCTTTTATGCCTATAATGTATCGTTATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCAAT-ATGCATTGTCATGC
*
37534 ATTTTTATTTATGGCATCCTTTCATGCCAA-ATGCATT
1 ATTTTCATTTATGGCATCCTTTCATGCCAATATGCATT
37571 TAACCTTTCA
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
44 5 0.07
45 1 0.01
46 61 0.91
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (45 bp):
ATTTTCATTTATGGCATCCTTTCATGCCAATATGCATTGTCATGC
Found at i:37666 original size:81 final size:81
Alignment explanation
Indices: 37568--38261 Score: 921
Period size: 81 Copynumber: 8.6 Consensus size: 81
37558 TGCCAAATGC
* * * * * * *
37568 ATTTAACCTTTCATCTAACTTGCATTATTGGCACATTTCTGCCTAATGCAGAGTTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
37633 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* *
37649 ATTTAACCTTTCATCTAA-TTGGCATGATTGACACCTTTTTGTCAAATGCATAGCTAGGCAATTA
1 ATTTAACCTTTCATCTAACTT-GCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTA
*
37713 GTCTTTTACTCAAAGGT
65 ATCTTTTACTCAAAGGT
* * * *
37730 ATTTAACCTTTCATCTAA-TTGGCATGATTGATACCTTTTTGTCAAATGCATAGCTAGACAATTA
1 ATTTAACCTTTCATCTAACTT-GCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTA
*
37794 GTCTTTTACTCAAAGGT
65 ATCTTTTACTCAAAGGT
* * * *
37811 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTTTGTCAAATACATAGCTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
37876 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * * * * *
37892 ATTTAACATTTCATCTAACTAGCAAGATTGACACATTTTTGTAAAATGCACAGCTAGGCAATTAG
1 ATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
37957 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * *
37973 ATTTAACCTTTCATCTAA-TTGGCATGATTAACA-CATTCATGTCAAATGCACAACTAGGCAATT
1 ATTTAACCTTTCATCTAACTT-GCATGATTGACACCTTTC-TGTCAAATGCACAGCTAGGCAATT
*
38036 AATATTTTACTCAAAGGT
64 AATCTTTTACTCAAAGGT
* * * * * * * *
38054 ATTTAACCATTCATCTAACTGGTATGATTGATACATTTATATCAAATGCACAACTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
*
38119 TCTTTTACTCATAGGT
66 TCTTTTACTCAAAGGT
* *
38135 ATTTAACATTTCATCTAAC-TGACATGATCGACACCTTTCTGTCAAATGCACAGCTAGGCAATTA
1 ATTTAACCTTTCATCTAACTTG-CATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTA
38199 ATCTTTTACTCAAAGGT
65 ATCTTTTACTCAAAGGT
* *
38216 ATTTAACCTTTTATCTAACTAGCATGATTGACACCTTTCTGTCAAA
1 ATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAA
38262 GGTATTTAAC
Statistics
Matches: 544, Mismatches: 61, Indels: 16
0.88 0.10 0.03
Matches are distributed among these distances:
80 6 0.01
81 533 0.98
82 5 0.01
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (81 bp):
ATTTAACCTTTCATCTAACTTGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
TCTTTTACTCAAAGGT
Found at i:38251 original size:27 final size:27
Alignment explanation
Indices: 38221--38302 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
38211 AAGGTATTTA
38221 ACCTTTTATCTAACTAGCATGATTGAC
1 ACCTTTTATCTAACTAGCATGATTGAC
* * *
38248 ACCTTTCTGTC-AA--AG-GT-ATTTA-
1 ACCTTT-TATCTAACTAGCATGATTGAC
* *
38270 ACCTTTCATCTAACTGGCATGATTGAC
1 ACCTTTTATCTAACTAGCATGATTGAC
38297 ACCTTT
1 ACCTTT
38303 CTGTCAAATG
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
21 2 0.05
22 8 0.20
23 4 0.10
24 2 0.05
25 3 0.08
26 4 0.10
27 14 0.35
28 3 0.08
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (27 bp):
ACCTTTTATCTAACTAGCATGATTGAC
Found at i:38264 original size:49 final size:49
Alignment explanation
Indices: 38208--38310 Score: 188
Period size: 49 Copynumber: 2.1 Consensus size: 49
38198 AATCTTTTAC
*
38208 TCAAAGGTATTTAACCTTTTATCTAACTAGCATGATTGACACCTTTCTG
1 TCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTG
*
38257 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTG
1 TCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTG
38306 TCAAA
1 TCAAA
38311 TGCACAACTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (49 bp):
TCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTG
Found at i:38301 original size:130 final size:130
Alignment explanation
Indices: 38131--38391 Score: 468
Period size: 130 Copynumber: 2.0 Consensus size: 130
38121 TTTTACTCAT
*
38131 AGGTATTTAACATTTCATCTAACTGACATGATCGACACCTTTCTGTCAAATGCACAGCTAGGCAA
1 AGGTATTTAACATTTCATCTAACTGACATGATCGACACCTTTCTGTCAAATGCACAACTAGGCAA
* *
38196 TTAATCTTTTACTCAAAGGTATTTAACCTTTTATCTAACTAGCATGATTGACACCTTTCTGTCAA
66 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTGTCAA
* * *
38261 AGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGGCAA
1 AGGTATTTAACATTTCATCTAACTGACATGATCGACACCTTTCTGTCAAATGCACAACTAGGCAA
38326 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTGTCAA
66 TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTGTCAA
38391 A
1 A
38392 TGCACTGCTA
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 125 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.35
Consensus pattern (130 bp):
AGGTATTTAACATTTCATCTAACTGACATGATCGACACCTTTCTGTCAAATGCACAACTAGGCAA
TTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTGTCAA
Found at i:38392 original size:81 final size:81
Alignment explanation
Indices: 38257--38490 Score: 405
Period size: 81 Copynumber: 2.9 Consensus size: 81
38247 CACCTTTCTG
38257 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAG
*
38322 GCAATTAATCTTTTAC
66 GCAATTAATCGTTTAC
* * **
38338 TCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCTGTCAAATGCACTGCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAG
38403 GCAATTAATCGTTTAC
66 GCAATTAATCGTTTAC
* *
38419 TCAAAGGTATTTAACTTTTCATCTAACTGGCATGATTAACACCTTTCTGTCAAATGCACAACTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAG
38484 GCAATTA
66 GCAATTA
38491 GTGTTTTATT
Statistics
Matches: 142, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 142 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (81 bp):
TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAG
GCAATTAATCGTTTAC
Found at i:38410 original size:211 final size:211
Alignment explanation
Indices: 38046--38472 Score: 696
Period size: 211 Copynumber: 2.0 Consensus size: 211
38036 AATATTTTAC
* *
38046 TCAAAGGTATTTAACCATTCATCTAACTGGTATGATTGATACATTTATATCAAATGCACAACTAG
1 TCAAAGGTATTTAACCATTCATCTAACTGGCATGATTGACACATTTATATCAAATGCACAACTAG
* *
38111 GCAATTAATCTTTTACTCATAGGTATTTAACATTTCATCTAACTGACATGATCGACACCTTTCTG
66 GCAATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATGATCGACACATTTCTG
*
38176 TCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTT-ATCTAACTAGCA
131 TCAAATGCACAGCTAGGCAATTAATCGTTTACTCAAAGGTATTTAA-CTTTTCATCTAACTAGCA
*
38240 TGATTGACACCTTTCTG
195 TGATTAACACCTTTCTG
* * * *
38257 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAG
1 TCAAAGGTATTTAACCATTCATCTAACTGGCATGATTGACACATTTATATCAAATGCACAACTAG
* *
38322 GCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-AGCATGATTGACACATTTCT
66 GCAATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGA-CATGATCGACACATTTCT
* *
38386 GTCAAATGCACTGCTAGGCAATTAATCGTTTACTCAAAGGTATTTAACTTTTCATCTAACTGGCA
130 GTCAAATGCACAGCTAGGCAATTAATCGTTTACTCAAAGGTATTTAACTTTTCATCTAACTAGCA
38451 TGATTAACACCTTTCTG
195 TGATTAACACCTTTCTG
38468 TCAAA
1 TCAAA
38473 TGCACAACTA
Statistics
Matches: 200, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
210 6 0.03
211 194 0.97
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.36
Consensus pattern (211 bp):
TCAAAGGTATTTAACCATTCATCTAACTGGCATGATTGACACATTTATATCAAATGCACAACTAG
GCAATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGACATGATCGACACATTTCTG
TCAAATGCACAGCTAGGCAATTAATCGTTTACTCAAAGGTATTTAACTTTTCATCTAACTAGCAT
GATTAACACCTTTCTG
Found at i:38489 original size:292 final size:292
Alignment explanation
Indices: 37965--38490 Score: 865
Period size: 292 Copynumber: 1.8 Consensus size: 292
37955 AGTCTTTTAC
*
37965 TCAAAGGTATTTAACCTTTCATCTAATTGGCATGATTAACACATTCATGTCAAATGCACAACTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTAACACATTCATGTCAAATGCACAACTAG
* * *
38030 GCAATTAATATTTTACTCAAAGGTATTTAACCATTCATCTAACTGGTATGATTGATACATTTATA
66 GCAATTAATATTTTACTCAAAGGTATTTAACCATTCATCTAACTAGCATGATTGACACATTTATA
* *
38095 TCAAATGCACAACTAGGCAATTAATCTTTTACTCATAGGTATTTAACATTTCATCTAACTGACAT
131 TCAAATGCACAACTAGGCAATTAATCGTTTACTCAAAGGTATTTAACATTTCATCTAACTGACAT
* *
38160 GATCGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCT
196 GATCAACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCT
38225 TTTATCTAACTAGCATGATTGACACCTTTCTG
261 TTTATCTAACTAGCATGATTGACACCTTTCTG
* *
38257 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTC-TGTCAAATGCACAACTA
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTAACA-CATTCATGTCAAATGCACAACTA
* * *
38321 GGCAATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCT
65 GGCAATTAATATTTTACTCAAAGGTATTTAACCATTCATCTAACTAGCATGATTGACACATTTAT
* ** * *
38386 GTCAAATGCACTGCTAGGCAATTAATCGTTTACTCAAAGGTATTTAACTTTTCATCTAACTGGCA
130 ATCAAATGCACAACTAGGCAATTAATCGTTTACTCAAAGGTATTTAACATTTCATCTAACTGACA
*
38451 TGATTAACACCTTTCTGTCAAATGCACAACTAGGCAATTA
195 TGATCAACACCTTTCTGTCAAATGCACAACTAGGCAATTA
38491 GTGTTTTATT
Statistics
Matches: 214, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
292 210 0.98
293 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (292 bp):
TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTAACACATTCATGTCAAATGCACAACTAG
GCAATTAATATTTTACTCAAAGGTATTTAACCATTCATCTAACTAGCATGATTGACACATTTATA
TCAAATGCACAACTAGGCAATTAATCGTTTACTCAAAGGTATTTAACATTTCATCTAACTGACAT
GATCAACACCTTTCTGTCAAATGCACAACTAGGCAATTAATCTTTTACTCAAAGGTATTTAACCT
TTTATCTAACTAGCATGATTGACACCTTTCTG
Found at i:39042 original size:94 final size:95
Alignment explanation
Indices: 38906--39085 Score: 276
Period size: 94 Copynumber: 1.9 Consensus size: 95
38896 CCATGGTATT
* * *
38906 GATACTTCTATATTGTGCTATCGATACTCCCTTGCAGTATCGATACCATTTCTATATTCTGG-AT
1 GATACTTCTATACTATGCTATCGATACTCCCTTGCAGTATCGATACCATTTCGATATTCTGGAAT
38970 CCATGGTATCGATACTTTCCTCCTAGTGCC
66 CCATGGTATCGATACTTTCCTCCTAGTGCC
*
39000 GATACTTCTATACTATGGTA-CTGATACTCCCATT-CAGTATCGATACCATTTCGATATTCTGGA
1 GATACTTCTATACTATGCTATC-GATACTCCC-TTGCAGTATCGATACCATTTCGATATTCTGGA
*
39063 ATCCATGGTATTGATACTTTCCT
64 ATCCATGGTATCGATACTTTCCT
39086 TTTTGTATCG
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
93 1 0.01
94 53 0.68
95 24 0.31
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (95 bp):
GATACTTCTATACTATGCTATCGATACTCCCTTGCAGTATCGATACCATTTCGATATTCTGGAAT
CCATGGTATCGATACTTTCCTCCTAGTGCC
Found at i:41004 original size:48 final size:48
Alignment explanation
Indices: 40933--41032 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 48
40923 TATAGTACTG
* *
40933 ATACGAAAATGCAACATATGCATTAAACAAAATTGATTAATAACCATC
1 ATACGAAAATGCAACATATGCATTAAACAAAATCGATCAATAACCATC
* * *
40981 ATACGAAAATGCAACTTATGCATTAAATAAAATCGATCGATAACCATC
1 ATACGAAAATGCAACATATGCATTAAACAAAATCGATCAATAACCATC
41029 ATAC
1 ATAC
41033 ACAAAGTATG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.18, G:0.09, T:0.25
Consensus pattern (48 bp):
ATACGAAAATGCAACATATGCATTAAACAAAATCGATCAATAACCATC
Found at i:41679 original size:20 final size:20
Alignment explanation
Indices: 41654--41704 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
41644 TTTTGTTTAC
41654 GGTATTGATACCTTCCTCAT
1 GGTATTGATACCTTCCTCAT
41674 GGTATTGATACCTTCCTCAT
1 GGTATTGATACCTTCCTCAT
*
41694 GGTATCGATAC
1 GGTATTGATAC
41705 TTCTTTCATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (20 bp):
GGTATTGATACCTTCCTCAT
Found at i:41733 original size:19 final size:21
Alignment explanation
Indices: 41695--41734 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41685 CTTCCTCATG
*
41695 GTATCGATACTTCTTTCATCA
1 GTATCGATACTTCGTTCATCA
41716 GTATCGATA-TT-GTTCATCA
1 GTATCGATACTTCGTTCATCA
41735 TGTTCGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (21 bp):
GTATCGATACTTCGTTCATCA
Found at i:44964 original size:2 final size:2
Alignment explanation
Indices: 44957--44993 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
44947 AGTTATTCCA
44957 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
44994 GTAGATGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46303 original size:2 final size:2
Alignment explanation
Indices: 46296--46320 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46286 CATAAACAAG
46296 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
46321 GAAAACCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47705 original size:2 final size:2
Alignment explanation
Indices: 47700--47740 Score: 64
Period size: 2 Copynumber: 19.5 Consensus size: 2
47690 TCCCATTTTT
47700 TA TA TA TA CTCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA -T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47741 TGCAAACGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 34 0.92
3 2 0.05
4 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:47888 original size:37 final size:37
Alignment explanation
Indices: 47721--48122 Score: 380
Period size: 37 Copynumber: 10.9 Consensus size: 37
47711 ATATATATAT
* * *
47721 ATATATATATATATATA-TATTGCAAACGGTTTTTGAAA
1 ATATATATA-ATATATAGTTTTGAAAAC-ATTTTTGAAA
* *
47759 ATGTATATAATATAT--TTTT-AAAACATTTTAGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* *
47793 AAATATAT-ATAATATAGTTTTTAAAATCA-TTTTG-AA
1 ATATATATAAT-ATATAGTTTTGAAAA-CATTTTTGAAA
*
47829 ATTTATATAATATA-A-TTTTGAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
*
47864 ATTTATATAATATATAGTTTTGAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
*
47901 ATTTATATAATATATAGTTTTGAAAACA-TTTTGAAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTG-AAA
* * * *
47938 CATTTATATATTATATAGTTTTTAAAA-ACGTTTTGAAA
1 -ATATATATAATATATAGTTTTGAAAACA-TTTTTGAAA
*
47976 ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
* * *
48013 ATATATATATTATATAATTTTTTAAAACATTTTTGAAA
1 ATATATATAATATAT-AGTTTTGAAAACATTTTTGAAA
* * * *
48051 ATACATATAATATATAATTTTTTAAAAAACA-TTTTGGAA
1 ATATATATAATATAT-A-GTTTT-GAAAACATTTTTGAAA
** *
48090 ATATATATAAT-TAATTTTTTTGAAAATATTTTT
1 ATATATATAATAT-ATAGTTTTGAAAACATTTTT
48123 ATTATTATTT
Statistics
Matches: 318, Mismatches: 26, Indels: 41
0.83 0.07 0.11
Matches are distributed among these distances:
33 4 0.01
34 31 0.10
35 21 0.07
36 29 0.09
37 123 0.39
38 75 0.24
39 29 0.09
40 6 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTGAAAACATTTTTGAAA
Found at i:47934 original size:11 final size:11
Alignment explanation
Indices: 47918--47942 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
47908 TAATATATAG
47918 TTTTGAAAACA
1 TTTTGAAAACA
47929 TTTTGAAAACA
1 TTTTGAAAACA
47940 TTT
1 TTT
47943 ATATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:47959 original size:75 final size:73
Alignment explanation
Indices: 47750--48098 Score: 399
Period size: 75 Copynumber: 4.7 Consensus size: 73
47740 TTGCAAACGG
* * * *
47750 TTTTTGAAAATGTATATAATATAT-TTTT-AAAACATTTTAGAAAAAATATATATAATATAGTTT
1 TTTTTGAAAATATATATAATATATATTTTGAAAACATTTTTGAAAATATATATATTATATAGTTT
47813 TTAAAATCA
66 TTAAAA-CA
* * *
47822 -TTTTG-AAATTTATATAATATA-ATTTTGAAAACATTTTTGAAAATTTATATAATATATAGTTT
1 TTTTTGAAAATATATATAATATATATTTTGAAAACATTTTTGAAAATATATATATTATATAGTTT
*
47884 TGAAAACA
66 TTAAAACA
* *
47892 TTTTTGAAAATTTATATAATATATAGTTTTGAAAACA-TTTTGAAAACATTTATATATTATATAG
1 TTTTTGAAAATATATATAATATATA-TTTTGAAAACATTTTTG-AAA-ATATATATATTATATAG
47956 TTTTTAAAA-A
63 TTTTTAAAACA
* * *
47966 CGTTTTGAAAATATATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATATTATATAAT
1 -TTTTTGAAAATATATATAATATATA-TTTTGAAAACATTTTTGAAAATATATATATTATAT-AG
48031 TTTTTAAAACA
63 TTTTTAAAACA
* * *
48042 TTTTTGAAAATACATATAATATATAATTTTTTAAAAAACA-TTTTGGAAATATATATA
1 TTTTTGAAAATATATATAATATAT-A--TTTT-GAAAACATTTTTGAAAATATATATA
48099 ATTAATTTTT
Statistics
Matches: 243, Mismatches: 19, Indels: 25
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.09
71 45 0.19
72 16 0.07
73 6 0.02
74 29 0.12
75 93 0.38
76 7 0.03
77 20 0.08
78 6 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (73 bp):
TTTTTGAAAATATATATAATATATATTTTGAAAACATTTTTGAAAATATATATATTATATAGTTT
TTAAAACA
Found at i:48165 original size:22 final size:20
Alignment explanation
Indices: 48116--48169 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
48106 TTTTTGAAAA
48116 TATTT-TTATTATTATTTAT
1 TATTTCTTATTATTATTTAT
*
48135 TATTATTCTTCTTATTATTTTATT
1 TA-T-TTCTTATTATTA-TTTA-T
48159 TATTTCTTATT
1 TATTTCTTATT
48170 TCTTATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.07
20 1 0.04
21 2 0.07
22 15 0.54
23 5 0.18
24 3 0.11
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (20 bp):
TATTTCTTATTATTATTTAT
Found at i:49433 original size:18 final size:20
Alignment explanation
Indices: 49412--49460 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
49402 CCTTATTTCC
49412 TTTAAAATTATTATT-A-TT
1 TTTAAAATTATTATTCATTT
*
49430 TTT-ATATT-TTATTCATTT
1 TTTAAAATTATTATTCATTT
49448 TTTATAAATTATT
1 TTTA-AAATTATT
49461 TTAAGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.21
17 5 0.21
18 8 0.33
20 4 0.17
21 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTAAAATTATTATTCATTT
Found at i:53469 original size:95 final size:95
Alignment explanation
Indices: 53350--53612 Score: 395
Period size: 95 Copynumber: 2.7 Consensus size: 95
53340 AAATTATAAT
* *
53350 ATTATATATATACAATAAATCTTGAGTTGTCCTTCTAAAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATATATATACAATAAA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
*
53415 TGGATAAGATTGAGCTAGCCTGATAAAGGTG
65 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
53446 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATATATATACAATAAA-CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
*
53510 TGGATAATATTCAGCTAGCCTGATAAAGGTG
65 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
* * *
53541 ATTATAATATTTATACAATGATA-TTAAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAGCT
1 ATTAT-ATA--TATACAAT-AAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCT
53605 TTATGGAT
62 TTATGGAT
53613 TCAGCTAGCC
Statistics
Matches: 154, Mismatches: 8, Indels: 8
0.91 0.05 0.05
Matches are distributed among these distances:
95 89 0.58
96 7 0.05
97 1 0.01
98 47 0.31
99 8 0.05
100 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (95 bp):
ATTATATATATACAATAAACTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
GGATAAGATTCAGCTAGCCTGATAAAGGTG
Found at i:54779 original size:84 final size:84
Alignment explanation
Indices: 54504--55665 Score: 1355
Period size: 84 Copynumber: 13.9 Consensus size: 84
54494 ACTATTGGCG
* * * * * * * * *
54504 GCATAACTCAAGGCTAGAAGGGTTATTTTCCAACAAAAGACCTTTGAGTTCAACTACGCTCAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
* *
54569 TAACGGCACATCATTTGCA
66 CAAAGGCACATCATTTGCA
* * * * * *
54588 ACATACCTTAAGTCGAGAAGGGCTATCAGCCAACCAAAGACCCTCGAGTTCGATTACACTCAGCG
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGC-
* * * *
54653 TCGAGGGTACATCATTTACA
65 TCAAAGGCACATCATTTGCA
* * * * * * *
54673 GCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
* *
54738 CAACGACACATCATTTGCA
66 CAAAGGCACATCATTTGCA
* * * *
54757 GCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
54822 CCAAA-GCACATCATTTGCA
66 -CAAAGGCACATCATTTGCA
* * * * * *
54841 GCATAACTCAAGGCTAGAAGGGTTATTTGTCAA-CAAAGACCTTCAAGTTCGATTACACTCAACT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
*
54905 CAAAGGCACAACATTTGCA
66 CAAAGGCACATCATTTGCA
* * * ** *
54924 GCATAGCTTAAGTCGAGAAGGGCTATCTATCATCCAAAGACCTTCGAGTTCGATTACACTCAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
* *
54989 CCAAGGCACATCATTTCCA
66 CAAAGGCACATCATTTGCA
* * * * *
55008 GCATAACTCAAGGCTAGAAGGGTTATCTACCAA-CAAAGACCTTCGAGTTTGATTACACTTAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
55072 CAAAGGCACATCATTTGCA
66 CAAAGGCACATCATTTGCA
* * * ** *
55091 GCATAGA-ATAAGTCTAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGACTATGCTCAAC
1 GCATA-ACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGC
*
55155 TCCAAGGCACATCATTTGCA
65 TCAAAGGCACATCATTTGCA
* * *
55175 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCGATTACACTCAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
*
55239 CAAAGGCACAACATTTGCA
66 CAAAGGCACATCATTTGCA
* * * * * **
55258 GCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTTGAGTTTAATTACACTCAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
* * *
55323 CCAAGACACATCATTTACA
66 CAAAGGCACATCATTTGCA
* * * *
55342 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-CAAAGACCTTCGAGTTCAATTACACTCAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
55406 CAAAGGCACATCATTTGCA
66 CAAAGGCACATCATTTGCA
* * * *
55425 GCATAGCTTAAGTCGAGAAGGGTTATCTGTCATCCAAAGACCTTCGAGTTCGATTACACTCAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
* **
55490 CCAAGATACATCATTTGCA
66 CAAAGGCACATCATTTGCA
* * * * * *
55509 GCATAACTCAAGGCTAGAAGGGTTATCTTCCAACAAAAGACCTTCTAGTTCGATTACACTCAACT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
* *
55574 CAAAGGCTCAACATTTGCA
66 CAAAGGCACATCATTTGCA
* * * * *
55593 GAATAGCTTAAGTCGAGAAGGGTTATCTGCCATCCAAAGACCTTCGAGTTCGATTACATTCAGCT
1 GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
*
55658 CAGAGGCA
66 CAAAGGCA
55666 AATAAAACTT
Statistics
Matches: 901, Mismatches: 168, Indels: 18
0.83 0.15 0.02
Matches are distributed among these distances:
82 4 0.00
83 281 0.31
84 547 0.61
85 69 0.08
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
GCATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACACTCAGCT
CAAAGGCACATCATTTGCA
Found at i:54963 original size:167 final size:167
Alignment explanation
Indices: 54504--55658 Score: 1625
Period size: 167 Copynumber: 6.9 Consensus size: 167
54494 ACTATTGGCG
* * * * *
54504 GCATAACTCAAGGCTAGAAGGGTTAT-TTTCCAACAAAAGACCTTTGAGTTCAACTACGCTCAGC
1 GCATAACTCAAGGCTAGAAGGGTTATCTGT-CAAC-AAAGACCTTCGAGTTCGATTACACTCAGC
* * * * * * *
54568 TTAACGGCACATCATTTGCAACATACCTTAAGTCGAGAAGGGCTATCAGCCAACCAAAGACCCTC
64 TCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTC
* ** * *
54633 GAGTTCGATTACACTCAGCGTCGAGGGTACATCATTTACA
129 GAGTTCGATTACACTCAGC-TCCAAAGCACATCATTTGCA
* * * * *
54673 GCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCT
1 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAGCT
* * * *
54738 CAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCG
65 CAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTCG
* *
54803 AGTTCGACTACGCTCAGCTCCAAAGCACATCATTTGCA
130 AGTTCGATTACACTCAGCTCCAAAGCACATCATTTGCA
* * *
54841 GCATAACTCAAGGCTAGAAGGGTTATTTGTCAACAAAGACCTTCAAGTTCGATTACACTCAACTC
1 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
* **
54906 AAAGGCACAACATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTATCATCCAAAGACCTTCGA
66 AAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTCGA
* *
54971 GTTCGATTACACTCAGCTCCAAGGCACATCATTTCCA
131 GTTCGATTACACTCAGCTCCAAAGCACATCATTTGCA
** * *
55008 GCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAGACCTTCGAGTTTGATTACACTTAGCTC
1 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
** * *
55073 AAAGGCACATCATTTGCAGCATAGAATAAGTCTAGAAGGGCTATCTGCCAACCAAAGACCTTCGA
66 AAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTCGA
* ** * *
55138 GTTCGACTATGCTCAACTCCAAGGCACATCATTTGCA
131 GTTCGATTACACTCAGCTCCAAAGCACATCATTTGCA
55175 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
1 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
55240 AAAGGCACAACATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTTGA
66 AAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTCGA
** *
55305 GTTTAATTACACTCAGCTCC-AAGACACATCATTTACA
131 GTTCGATTACACTCAGCTCCAAAG-CACATCATTTGCA
*
55342 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCAATTACACTCAGCTC
1 GCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
* *
55407 AAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGTCATCCAAAGACCTTCGA
66 AAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTCGA
*
55472 GTTCGATTACACTCAGCTCC-AAGATACATCATTTGCA
131 GTTCGATTACACTCAGCTCCAAAG-CACATCATTTGCA
* *
55509 GCATAACTCAAGGCTAGAAGGGTTATCT-TCCAACAAAAGACCTTCTAGTTCGATTACACTCAAC
1 GCATAACTCAAGGCTAGAAGGGTTATCTGT-CAAC-AAAGACCTTCGAGTTCGATTACACTCAGC
* * * *
55573 TCAAAGGCTCAACATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTGCCATCCAAAGACCTTC
64 TCAAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTC
*
55638 GAGTTCGATTACATTCAGCTC
129 GAGTTCGATTACACTCAGCTC
55659 AGAGGCAAAT
Statistics
Matches: 891, Mismatches: 91, Indels: 9
0.90 0.09 0.01
Matches are distributed among these distances:
166 3 0.00
167 600 0.67
168 154 0.17
169 133 0.15
170 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (167 bp):
GCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAGCTC
AAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCATCCAAAGACCTTCGA
GTTCGATTACACTCAGCTCCAAAGCACATCATTTGCA
Found at i:56376 original size:75 final size:71
Alignment explanation
Indices: 56297--56546 Score: 248
Period size: 75 Copynumber: 3.5 Consensus size: 71
56287 TGTAAACGGT
*
56297 TTTTGAAAATGTATATAATATATAGTTTTAAAAAAACACTTTTGAAAACTATCTAATATATAGTT
1 TTTTGAAAATATATATAATATATAGTTTT-AAAAAACA-TTTTGAAAA-TAT-TAATATATAGTT
56362 TTTAAAATCA
62 TTTAAAATCA
* *
56372 TTTTGAAAACT-TATATAATATATAGTTTT-GAAAACA-TTT----ATA-TATTATATAGTTTTT
1 TTTTGAAAA-TATATATAATATATAGTTTTAAAAAACATTTTGAAAATATTAATATATAGTTTTT
* *
56429 AAAAACG
65 AAAATCA
** *
56436 TTTTGAAAATATATATAATATATAGTTTTTTAAAACATTTTTGAAAATATATATATTATATAATT
1 TTTTGAAAATATATATAATATATAGTTTTAAAAAACA-TTTTGAAAATAT-TA-A-TATATAGTT
56501 TTT-AAATCA
62 TTTAAAATCA
* *
56510 TTTTTGAAAATACATATAATATATAATTTTTAAAAAA
1 -TTTTGAAAATATATATAATATAT-AGTTTTAAAAAA
56547 AACATATTAG
Statistics
Matches: 147, Mismatches: 13, Indels: 29
0.78 0.07 0.15
Matches are distributed among these distances:
63 1 0.01
64 46 0.31
65 6 0.04
66 2 0.01
67 4 0.03
71 6 0.04
73 8 0.05
74 4 0.03
75 60 0.41
76 10 0.07
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (71 bp):
TTTTGAAAATATATATAATATATAGTTTTAAAAAACATTTTGAAAATATTAATATATAGTTTTTA
AAATCA
Found at i:56400 original size:25 final size:26
Alignment explanation
Indices: 56372--56432 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 26
56362 TTTAAAATCA
56372 TTTTGAAAAC-TTATATAATATATAG
1 TTTTGAAAACATTATATAATATATAG
*
56397 TTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAACA-TTATATAATATATAG
*
56424 TTTTTAAAA
1 TTTTGAAAA
56433 ACGTTTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 10 0.31
27 22 0.69
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (26 bp):
TTTTGAAAACATTATATAATATATAG
Found at i:56400 original size:37 final size:37
Alignment explanation
Indices: 56268--56544 Score: 251
Period size: 37 Copynumber: 7.7 Consensus size: 37
56258 ATATACATAC
* * *
56268 ATATATATATTATATAGTTTGT-AAACGGTTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAAC-ATTTTTGAAA
* * *
56305 ATGTATATAATATATAGTTTTAAAAAAACACTTTTGAAA
1 ATATATATAATATATAGTTTT--TAAAACATTTTTGAAA
* *
56344 A-CTATCTAATATATAGTTTTTAAAATCA-TTTTGAAA
1 ATATATATAATATATAGTTTTTAAAA-CATTTTTGAAA
*
56380 ACT-TATATAATATATAGTTTTGAAAACA---TT----
1 A-TATATATAATATATAGTTTTTAAAACATTTTTGAAA
*
56410 -TATATAT--TATATAGTTTTTAAAA-ACGTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACA-TTTTTGAAA
56444 ATATATATAATATATAGTTTTTTAAAACATTTTTGAAA
1 ATATATATAATATATAG-TTTTTAAAACATTTTTGAAA
* * *
56482 ATATATATATTATATAATTTTTAAATCATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
* *
56519 ATACATATAATATATAATTTTTAAAA
1 ATATATATAATATATAGTTTTTAAAA
56545 AAAACATATT
Statistics
Matches: 201, Mismatches: 19, Indels: 40
0.77 0.07 0.15
Matches are distributed among these distances:
26 1 0.00
27 15 0.07
28 1 0.00
29 5 0.02
30 2 0.01
34 2 0.01
35 7 0.03
36 15 0.07
37 90 0.45
38 49 0.24
39 10 0.05
40 4 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTAAAACATTTTTGAAA
Found at i:56421 original size:64 final size:65
Alignment explanation
Indices: 56353--56475 Score: 196
Period size: 64 Copynumber: 1.9 Consensus size: 65
56343 AACTATCTAA
*
56353 TATATAGTTTTTAAAATCATTTTGAAAACT-TATATAATATATAG-TTTTGAAAACATTTATATA
1 TATATAGTTTTTAAAAACATTTTGAAAA-TATATATAATATATAGTTTTTGAAAACATTTATATA
56416 T
65 T
* *
56417 TATATAGTTTTTAAAAACGTTTTGAAAATATATATAATATATAGTTTTTTAAAACATTT
1 TATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACATTT
56476 TTGAAAATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
63 1 0.02
64 40 0.74
65 13 0.24
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (65 bp):
TATATAGTTTTTAAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTATATAT
Found at i:56426 original size:139 final size:138
Alignment explanation
Indices: 56266--56544 Score: 361
Period size: 139 Copynumber: 2.0 Consensus size: 138
56256 ATATATACAT
*
56266 ACATATATATATTATATAGTTTGT-AAACGGTTTTTGAAAATGTATATAATATATAGTTTTAAAA
1 ACATATATATATTATATAGTTTGTAAAAC-G-TTTTGAAAATATATATAATATATAGTTTT-AAA
* * *
56330 AAACACTTTTGAAAACTATCTA-A-TATATAGTTTTTAAAATCA-TTTTGAAAACT-TATATAAT
63 AAACACTTTTGAAAA-TATATATATTATATAATTTTT-AAATCATTTTTGAAAA-TACATATAAT
*
56391 ATATAGTTTTGAAA
125 ATATAATTTTGAAA
* * **
56405 ACATTTATATATTATATAGTTTTTAAAAACGTTTTGAAAATATATATAATATATAGTTTTTTAAA
1 ACATATATATATTATATAGTTTGT-AAAACGTTTTGAAAATATATATAATATATAGTTTTAAAAA
*
56470 ACATTTTTGAAAATATATATATTATATAATTTTTAAATCATTTTTGAAAATACATATAATATATA
65 ACACTTTTGAAAATATATATATTATATAATTTTTAAATCATTTTTGAAAATACATATAATATATA
*
56535 ATTTTTAAA
130 ATTTTGAAA
56544 A
1 A
56545 AAAACATATT
Statistics
Matches: 123, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
137 5 0.04
138 23 0.19
139 90 0.73
140 1 0.01
141 4 0.03
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (138 bp):
ACATATATATATTATATAGTTTGTAAAACGTTTTGAAAATATATATAATATATAGTTTTAAAAAA
CACTTTTGAAAATATATATATTATATAATTTTTAAATCATTTTTGAAAATACATATAATATATAA
TTTTGAAA
Found at i:56578 original size:75 final size:74
Alignment explanation
Indices: 56410--56584 Score: 192
Period size: 75 Copynumber: 2.3 Consensus size: 74
56400 TGAAAACATT
* * * *
56410 TATATATTATATAGTTTTTAAAAACGTTTTGAAAATATATATAATATATAGTTTTTTAAAACATT
1 TATATATTATATA-TTTTTAAAAACGTTTTGAAAATACATATAATATATAATTTTTAAAAACATA
*
56475 TTTGAAAATA
65 TTAGAAAATA
* *
56485 TATATATTATATAATTTTT-AAATCATTTTTGAAAATACATATAATATATAATTTTTAAAAAAAA
1 TATATATTATAT-ATTTTTAAAAAC-GTTTTGAAAATACATATAATATATAATTTTT---AAAAA
*
56549 CATATTAG-AAATG
61 CATATTAGAAAATA
* *
56562 TATATATTATATTTTTTTGAAAA
1 TATATATTATATATTTTTAAAAA
56585 TATTTTATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
74 4 0.05
75 45 0.54
76 6 0.07
77 19 0.23
78 10 0.12
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (74 bp):
TATATATTATATATTTTTAAAAACGTTTTGAAAATACATATAATATATAATTTTTAAAAACATAT
TAGAAAATA
Found at i:56595 original size:3 final size:3
Alignment explanation
Indices: 56585--56616 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
56575 TTTTTGAAAA
56585 TAT T-T TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
56617 TCTTATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:61144 original size:72 final size:72
Alignment explanation
Indices: 61022--61161 Score: 271
Period size: 72 Copynumber: 1.9 Consensus size: 72
61012 ATCATAAATC
*
61022 AGATCCTGGTATGGGGATTTGTTGAACATCTCGTCTGAAACAGGGGGTGCCGTAGTTAAGCAGAG
1 AGATACTGGTATGGGGATTTGTTGAACATCTCGTCTGAAACAGGGGGTGCCGTAGTTAAGCAGAG
61087 GGAAAGA
66 GGAAAGA
61094 AGATACTGGTATGGGGATTTGTTGAACATCTCGTCTGAAACAGGGGGTGCCGTAGTTAAGCAGAG
1 AGATACTGGTATGGGGATTTGTTGAACATCTCGTCTGAAACAGGGGGTGCCGTAGTTAAGCAGAG
61159 GGA
66 GGA
61162 GCTAGATGTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.27, C:0.14, G:0.35, T:0.24
Consensus pattern (72 bp):
AGATACTGGTATGGGGATTTGTTGAACATCTCGTCTGAAACAGGGGGTGCCGTAGTTAAGCAGAG
GGAAAGA
Done.