Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001659.1 Hibiscus syriacus cultivar Beakdansim tig00003317_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: 106215
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:11686 original size:21 final size:21
Alignment explanation
Indices: 11660--11709 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
11650 TCCAGATTCC
11660 CAACGCGAACATCGACTATCG
1 CAACGCGAACATCGACTATCG
*
11681 CAACGCGAACTTCGACTATCG
1 CAACGCGAACATCGACTATCG
*
11702 CAATGCGA
1 CAACGCGA
11710 TTTTCCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.16
Consensus pattern (21 bp):
CAACGCGAACATCGACTATCG
Found at i:11729 original size:19 final size:19
Alignment explanation
Indices: 11705--11764 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
11695 ACTATCGCAA
11705 TGCGATTTTCCAAATTCGT
1 TGCGATTTTCCAAATTCGT
** *
11724 TGCGATAGTCCAAGTTCACGT
1 TGCGATTTTCCAAATT--CGT
11745 TGCGATTTATTCCAAATTCG
1 TGCGA-TT-TTCCAAATTCG
11765 CATTGCGATA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
19 13 0.42
21 10 0.32
22 1 0.03
23 7 0.23
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (19 bp):
TGCGATTTTCCAAATTCGT
Found at i:11770 original size:23 final size:22
Alignment explanation
Indices: 11699--11773 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
11689 ACTTCGACTA
*
11699 TCGCAATGCGATT-TTCCAAAT
1 TCGCATTGCGATTATTCCAAAT
* *
11720 TCG--TTGCGA-TAGTCCAAGT
1 TCGCATTGCGATTATTCCAAAT
* *
11739 TCACGTTGCGATTTATTCCAAAT
1 TCGCATTGCGA-TTATTCCAAAT
11762 TCGCATTGCGAT
1 TCGCATTGCGAT
11774 AGTCCAAGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
18 1 0.02
19 13 0.32
21 9 0.22
22 1 0.02
23 17 0.41
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (22 bp):
TCGCATTGCGATTATTCCAAAT
Found at i:11802 original size:63 final size:63
Alignment explanation
Indices: 11699--12030 Score: 279
Period size: 63 Copynumber: 5.3 Consensus size: 63
11689 ACTTCGACTA
* ** * * *
11699 TCGCAATGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAAT
1 TCGCATTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAAT
* * * *
11762 TCGCATTGCGATAGTCCAAGTTTGTTGGGATAGTCGAAGTTCGTGTTGCGATATATTCCAAAT
1 TCGCATTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAAT
* *
11825 T--CATTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAGT
1 TCGCATTGCGATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAAT
* * * ** * * * *
11888 TCG--TTTCGATAGTCGAAGTTCGCGTTGCAATTTTTTCCAAGTT--CGTTGC-A-ATAGTCGAA
1 TCGCATTGCGATAGTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAA
*
11947 GT
62 AT
* * * * *
11949 TCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGATTTATTCTAAGT
1 TCGCATTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAAT
12014 TCG--TTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
12031 AATCGCAACG
Statistics
Matches: 216, Mismatches: 39, Indels: 30
0.76 0.14 0.11
Matches are distributed among these distances:
61 45 0.21
62 1 0.00
63 141 0.65
64 1 0.00
65 28 0.13
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (63 bp):
TCGCATTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAAT
Found at i:11842 original size:105 final size:102
Alignment explanation
Indices: 11705--12002 Score: 341
Period size: 105 Copynumber: 2.9 Consensus size: 102
11695 ACTATCGCAA
*
11705 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAATTCGCATTG
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCGC-TTG
* * *
11770 CGATAGTCCAAGTTTGTTGGGATAGTCGAAGTTCGTGT
65 CGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* * *
11808 TGCGATATATTCCAAATTCATTGCGATAGTCCAAGTTCACGTTGCGA--TAGTCGAAGTTCGCGT
1 TGCGAT-T-TTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCGC-T
* * *
11871 TGTGATTTATTCCAAGTTCGTTTCGATAGTCGAAGTTCGCGT
63 TGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* * * * *
11913 TGCAATTTTTTCCAAGTTCGTTGCAATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG-TT
1 TGCGA--TTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCGCTT
*
11977 GCGATAGTCGAAGTTCGCATTGCGAT
64 GCGATAGTCCAAGTTCG--TTGCGAT
12003 TTATTCTAAG
Statistics
Matches: 162, Mismatches: 23, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
103 33 0.20
104 1 0.01
105 115 0.71
106 1 0.01
107 12 0.07
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (102 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCGCTTGC
GATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:12037 original size:42 final size:42
Alignment explanation
Indices: 11705--12027 Score: 315
Period size: 42 Copynumber: 7.7 Consensus size: 42
11695 ACTATCGCAA
* * *
11705 TGCGA-TT-TTCCAAATTCGTTGCGATAGTCCAAGTTCACGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* * *
11745 TGCGATTTATTCCAAATTCGCATTGCGATAGTCCAAGTT--TGT
1 TGCGATTTATTCCAAGTTCG--TTGCGATAGTCGAAGTTCGCGT
* * * * * * *
11787 TGGGA--TAGTCGAAGTTCGTGTTGCGATATATTCCAAATT--CAT
1 TGCGATTTATTCCAAGTTC--GTTGCG--ATAGTCGAAGTTCGCGT
*
11829 TGCGA--TAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGT
* *
11871 TGTGATTTATTCCAAGTTCGTTTCGATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
* * *
11913 TGCAATTTTTTCCAAGTTCGTTGCAATAGTCGAAGTTCGCGT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
11955 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCAT
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
*
11997 TGCGATTTATTCTAAGTTCGTTGCGATAGTC
1 TGCGATTTATTCCAAGTTCGTTGCGATAGTC
12028 CAAAATCGCA
Statistics
Matches: 241, Mismatches: 28, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
40 28 0.12
41 2 0.01
42 183 0.76
44 28 0.12
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.37
Consensus pattern (42 bp):
TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGT
Found at i:16153 original size:3 final size:3
Alignment explanation
Indices: 16145--16204 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
16135 ACAAATGCAC
16145 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
16193 TTA TTA TCA TTA
1 TTA TTA TTA TTA
16205 ACTTAATATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:16395 original size:18 final size:18
Alignment explanation
Indices: 16372--16420 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
16362 GCGTAGAATT
*
16372 TGTCCCGAAGGGCCACTA
1 TGTCCCGAAGGACCACTA
16390 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
16408 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
16421 TACATAGAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.33, G:0.27, T:0.16
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:16723 original size:21 final size:23
Alignment explanation
Indices: 16680--16723 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
16670 CATATATTCA
*
16680 CATATACATGTTCTAATATAATT
1 CATATACATGTTCTAATACAATT
*
16703 CATAT-CAT-TTCTCATACAATT
1 CATATACATGTTCTAATACAATT
16724 ACTTCATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.36, C:0.18, G:0.02, T:0.43
Consensus pattern (23 bp):
CATATACATGTTCTAATACAATT
Found at i:20724 original size:18 final size:18
Alignment explanation
Indices: 20703--20740 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
20693 GTCCTGAATG
*
20703 ACCACTATGTCCCGAGGA
1 ACCACTATGTCCCGAAGA
20721 ACCACTATGTCCCGAAGA
1 ACCACTATGTCCCGAAGA
20739 AC
1 AC
20741 TACATAGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.34, G:0.18, T:0.16
Consensus pattern (18 bp):
ACCACTATGTCCCGAAGA
Found at i:21037 original size:21 final size:23
Alignment explanation
Indices: 21001--21044 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
20991 ATATATTTCA
*
21001 CATATACATGTTCTCATATAATT
1 CATATACATGTTCTCATACAATT
21024 CATAT-CAT-TTCTCATACAATT
1 CATATACATGTTCTCATACAATT
21045 ACTTCATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 3 0.15
23 5 0.25
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.43
Consensus pattern (23 bp):
CATATACATGTTCTCATACAATT
Found at i:24552 original size:88 final size:88
Alignment explanation
Indices: 24404--24580 Score: 320
Period size: 88 Copynumber: 2.0 Consensus size: 88
24394 GCAAACCTAA
24404 GAGTAAAGAGCTCAGTAACAAAATATAACTTTGCTGAAAATCCAGATTCCAACGACGCCTCTCCA
1 GAGTAAAGAGCTCAGTAACAAAATATAACTTTGCTGAAAATCCAGATTCCAACGACGCCTCTCCA
24469 TTGCTTTTA-TCTTTTTGCATCT
66 TTGCTTTTAGTCTTTTTGCATCT
*
24491 GAGTAAAGAGCTCAGTAACAAAATAGTAACTTTGCTGAAAATCCAGATTCCACCGACGCCTCTCC
1 GAGTAAAGAGCTCAGTAACAAAATA-TAACTTTGCTGAAAATCCAGATTCCAACGACGCCTCTCC
24556 ATTGCTTTTATGTCTTTTTGCATCT
65 ATTGCTTTTA-GTCTTTTTGCATCT
24581 TTCTCAAATC
Statistics
Matches: 86, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
87 25 0.29
88 48 0.56
90 13 0.15
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (88 bp):
GAGTAAAGAGCTCAGTAACAAAATATAACTTTGCTGAAAATCCAGATTCCAACGACGCCTCTCCA
TTGCTTTTAGTCTTTTTGCATCT
Found at i:24814 original size:3 final size:3
Alignment explanation
Indices: 24808--24851 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
24798 TTTTTTATAC
*
24808 TAT TAT TAGT TAT TAT T-T TAT TAT TAT TAT TAT CAT TAT TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
24852 ATTAAATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:26985 original size:15 final size:16
Alignment explanation
Indices: 26950--26980 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
26940 AATGCAGACC
26950 ATTTTTCTTTAAAATG
1 ATTTTTCTTTAAAATG
26966 ATTTTTCTTTAAAAT
1 ATTTTTCTTTAAAAT
26981 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTTCTTTAAAATG
Found at i:28092 original size:30 final size:30
Alignment explanation
Indices: 28056--28116 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
28046 TCTTGCTTGA
*
28056 ACTAACTCGTTTTTCTCTTTTGTTTGTGTT
1 ACTAACTCGTTTTGCTCTTTTGTTTGTGTT
28086 ACTAACTCGTTTTGCTCTTTTGTTTGTGTT
1 ACTAACTCGTTTTGCTCTTTTGTTTGTGTT
28116 A
1 A
28117 TTTTTTAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.11, C:0.16, G:0.15, T:0.57
Consensus pattern (30 bp):
ACTAACTCGTTTTGCTCTTTTGTTTGTGTT
Found at i:31168 original size:11 final size:11
Alignment explanation
Indices: 31140--31177 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
31130 AAGAGCAAAG
31140 AGAAAAATCAA
1 AGAAAAATCAA
31151 AGCAAAAATCAA
1 AG-AAAAATCAA
*
31163 AGAAAAAGCAA
1 AGAAAAATCAA
31174 AGAA
1 AGAA
31178 CAAAAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:32364 original size:4 final size:4
Alignment explanation
Indices: 32355--32404 Score: 86
Period size: 4 Copynumber: 13.0 Consensus size: 4
32345 AAAAGTATAC
32355 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
32401 ACAT
1 ACAT
32405 GATACACAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
4 42 0.95
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:32531 original size:30 final size:30
Alignment explanation
Indices: 32495--32759 Score: 138
Period size: 30 Copynumber: 8.1 Consensus size: 30
32485 AAAAAAAAAA
32495 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
32525 AAAAATCTTTGAG-TTGGTTTC-TTTGAAAAC
1 AAAAATCTTTGAGATT-GTTTCTTTTG-AAAC
* * **
32555 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTCTTTTGAAAC
* *
32592 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
* * **
32622 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTCTTTTGAAAC
* *
32659 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
* * ***
32689 AAAATTTTGTCTCTCTTAAGACAATTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTCTTTTGAAAC
* *
32726 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
32756 AAAA
1 AAAA
32760 TTTTGTCTCT
Statistics
Matches: 174, Mismatches: 36, Indels: 50
0.67 0.14 0.19
Matches are distributed among these distances:
29 6 0.03
30 88 0.51
31 9 0.05
36 9 0.05
37 57 0.33
38 5 0.03
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTTGAAAC
Found at i:32591 original size:67 final size:67
Alignment explanation
Indices: 32512--32836 Score: 534
Period size: 67 Copynumber: 4.9 Consensus size: 67
32502 TTTGAGATTG
* *
32512 TTTCTTTTGAAACAAAAATCTTTGAGTTGGTTTCTTTGAAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
32577 AA
66 AA
32579 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
32644 AA
66 AA
*
32646 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAC
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
32711 AA
66 AA
32713 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
32778 AA
66 AA
* * * *
32780 TTGCTTTTG-AA-AAAAATCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTCTCTCTT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCTCTT
32837 GAGACAGTTT
Statistics
Matches: 248, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
63 1 0.00
64 18 0.07
65 20 0.08
66 4 0.02
67 205 0.83
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.45
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:32752 original size:134 final size:133
Alignment explanation
Indices: 32512--32878 Score: 539
Period size: 134 Copynumber: 2.8 Consensus size: 133
32502 TTTGAGATTG
* *
32512 TTTCTTTTGAAACAAAAATCTTTGAGTTGGTTTCTTTGAAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTG-AAACAAAATTTTGTCTCTCTTAAGAC
32577 AATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAG
65 AATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAG
32642 ATAA
130 ATAA
32646 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAC
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTT-GAAACAAAATTTTGTCTCTCTTAAGAC
32711 AATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAG
65 AATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAG
32776 ATAA
130 ATAA
* * * * *
32780 TTGCTTTTG-AA-AAAAATCTTTGAATCTGTTTCTCTT-AAA-ATGAATTTTGTCTCTCTTGAGA
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGAAACA-AAATTTTGTCTCTCTTAAGA
* * * * * *
32841 CAGTTTCTCTTG--AGATAAATCTTTGAGTCTGTTCCTTT
64 CAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTT
32879 TGAATAAAAA
Statistics
Matches: 217, Mismatches: 13, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
129 22 0.10
130 1 0.00
131 31 0.14
132 20 0.09
133 4 0.02
134 138 0.64
135 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (133 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGAAACAAAATTTTGTCTCTCTTAAGACA
ATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
TAA
Found at i:32861 original size:64 final size:64
Alignment explanation
Indices: 32512--32878 Score: 443
Period size: 67 Copynumber: 5.5 Consensus size: 64
32502 TTTGAGATTG
32512 TTTCTTTTGAAACAAAAATCTTTGAGT-TGGTTTCTTTGAAAACAAAATTTTGTCTCTCTTAAGA
1 TTTCTTTTG-AA-AAAAATCTTTGAGTCT-GTTTCTTTG-AAACAAAATTTTGTCTCTCTTAAGA
*
32576 TAA
62 CAA
* *
32579 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTG-AA-AAAAATCTTTGAGTCTGTTTCTTT-GAAACAAAATTTTGTCTCTCTTAAGAC
32644 AA
63 AA
*
32646 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAC
1 TTTCTTTTG-AA-AAAAATCTTTGAGTCTGTTTCTTT-GAAACAAAATTTTGTCTCTCTTAAGAC
32711 AA
63 AA
* *
32713 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTG-AA-AAAAATCTTTGAGTCTGTTTCTTT-GAAACAAAATTTTGTCTCTCTTAAGAC
32778 AA
63 AA
* * * *
32780 TTGCTTTTGAAAAAAATCTTTGAATCTGTTTCTCTT-AAA-ATGAATTTTGTCTCTCTTGAGACA
1 TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCT-TTGAAACA-AAATTTTGTCTCTCTTAAGACA
*
32843 G
64 A
* * * *
32844 TTTCTCTTGAGATAAATCTTTGAGTCTGTTCCTTT
1 TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTT
32879 TGAATAAAAA
Statistics
Matches: 281, Mismatches: 15, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
63 3 0.01
64 49 0.17
65 20 0.07
66 4 0.01
67 203 0.72
68 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (64 bp):
TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTGAAACAAAATTTTGTCTCTCTTAAGACAA
Found at i:32894 original size:29 final size:29
Alignment explanation
Indices: 32857--32928 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
32847 CTCTTGAGAT
32857 AAATCTTTGAGTCTGTTCCTTTTGAATA-A
1 AAATCTTTGAGTCTGTTCCTTTTGAA-ACA
*
32886 AAATCTTTGAGT-TGTTTCTTTTGAAACA
1 AAATCTTTGAGTCTGTTCCTTTTGAAACA
*
32914 AATCTCTTTGAGTCT
1 AA-ATCTTTGAGTCT
32929 ATTTCTGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 1 0.03
28 15 0.39
29 21 0.55
30 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
AAATCTTTGAGTCTGTTCCTTTTGAAACA
Found at i:32943 original size:30 final size:29
Alignment explanation
Indices: 32889--32945 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
32879 TGAATAAAAA
* * *
32889 TCTTTGAGTTGTTTCTTTTGAAACAAATC
1 TCTTTGAGTTATTTCTGTTAAAACAAATC
32918 TCTTTGAGTCTATTTCTGTTAAAACAAA
1 TCTTTGAGT-TATTTCTGTTAAAACAAA
32946 GTTTTGTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (29 bp):
TCTTTGAGTTATTTCTGTTAAAACAAATC
Found at i:33038 original size:60 final size:61
Alignment explanation
Indices: 32918--33040 Score: 194
Period size: 61 Copynumber: 2.0 Consensus size: 61
32908 GAAACAAATC
* *
32918 TCTTTGAGTCTATTTCTGTTAAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTAAAAAA
1 TCTTTGAGTCTATTTATGTTAAAACAAAGTTTTGTCTCTCTTGAAACAATTTCGTAAAAAA
* *
32979 TCTTTGAGTCTATTTATTTTGAAACAAAG-TTTGTCTCTCTTGAAACAATTTCGTGAAAAAA
1 TCTTTGAGTCTATTTATGTTAAAACAAAGTTTTGTCTCTCTTGAAACAATTTCGT-AAAAAA
33040 T
1 T
33041 ATGTGAGTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
60 24 0.42
61 33 0.58
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (61 bp):
TCTTTGAGTCTATTTATGTTAAAACAAAGTTTTGTCTCTCTTGAAACAATTTCGTAAAAAA
Found at i:33074 original size:27 final size:27
Alignment explanation
Indices: 33034--33100 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
33024 CAATTTCGTG
*
33034 AAAAAATATGTGAGT-TGTTTCTTTAGA
1 AAAAAAT-TTTGAGTCTGTTTCTTTAGA
*
33061 AAAAAATCTTTGAGTCTGTTTCTTTGGA
1 AAAAAAT-TTTGAGTCTGTTTCTTTAGA
33089 AACAAAATTTTG
1 AA-AAAATTTTG
33101 TCTCTCTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 13 0.37
28 17 0.49
29 5 0.14
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.40
Consensus pattern (27 bp):
AAAAAATTTTGAGTCTGTTTCTTTAGA
Found at i:33100 original size:149 final size:154
Alignment explanation
Indices: 32884--33174 Score: 387
Period size: 149 Copynumber: 1.9 Consensus size: 154
32874 CCTTTTGAAT
* * * * *
32884 AAAAATCTTTGAGTTGTTTCTTTTGAAACAAATCTCTTTGAGTCTATTTCTGTTAAAACAAAGTT
1 AAAAATATGTGAGTTGTTTCTTTAGAAACAAATATCTTTGAGTCTATTTCTGTTAAAACAAAATT
* **
32949 TTGTCTCTCTTGAGACAATTTC-GT-AAAA-AATCTTTGAGTCTATTTATTTTGAAACAAAGTTT
66 TTGTCTCTCTTGAGACAATTTCTGTGAAAATAATCTTTGAGTATATTTATTTAAAAACAAAGTTT
33011 GTCTCTCTTGAAACAATTTCGTGA
131 GTCTCTCTTGAAACAATTTCGTGA
* *
33035 AAAAATATGTGAGTTGTTTCTTTAGAAA-AAA-ATCTTTGAGTCTGTTTCT-TTGGAAACAAAAT
1 AAAAATATGTGAGTTGTTTCTTTAGAAACAAATATCTTTGAGTCTATTTCTGTT-AAAACAAAAT
* * * *
33097 TTTGTCTCTCTTGAGACAATTTCTTTTGAAAATCATCTTTGAGTATATTTCTTTAAAAACAAATT
65 TTTGTCTCTCTTGAGACAATTTC-TGTGAAAATAATCTTTGAGTATATTTATTTAAAAACAAAGT
*
33162 TTGTTTCTCTTGA
129 TTGTCTCTCTTGA
33175 GATAGTTTCT
Statistics
Matches: 120, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
148 2 0.02
149 47 0.39
150 3 0.03
151 26 0.22
152 4 0.03
153 38 0.32
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (154 bp):
AAAAATATGTGAGTTGTTTCTTTAGAAACAAATATCTTTGAGTCTATTTCTGTTAAAACAAAATT
TTGTCTCTCTTGAGACAATTTCTGTGAAAATAATCTTTGAGTATATTTATTTAAAAACAAAGTTT
GTCTCTCTTGAAACAATTTCGTGA
Found at i:33128 original size:65 final size:62
Alignment explanation
Indices: 33051--33242 Score: 177
Period size: 65 Copynumber: 3.0 Consensus size: 62
33041 ATGTGAGTTG
*
33051 TTTCTTTAGAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAA
1 TTTCTTTTGAAAAAAATCTTTGAGT-TGTTTCTTT-GAAAC-AAATTTTGTCTCTCTTGAGACAA
** * * * * *
33116 TTTCTTTTGAAAATCATCTTTGAGTATATTTCTTTAAAAACAAATTTTGTTTCTCTTGAGATAG
1 TTTCTTTTGAAAAAAATCTTTGAGT-TGTTTCTTT-GAAACAAATTTTGTCTCTCTTGAGACAA
** * * * * *
33180 TTTCTAATGAAAAATAACCTTTGGGATTGTTTCATTTGAAACAAATTTCGTCTCACTTAAGAC
1 TTTCTTTTGAAAAA-AATCTTTGAG-TTGTTTC-TTTGAAACAAATTTTGTCTCTCTTGAGAC
33243 GTGATCCATC
Statistics
Matches: 101, Mismatches: 23, Indels: 6
0.78 0.18 0.05
Matches are distributed among these distances:
64 31 0.31
65 66 0.65
66 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (62 bp):
TTTCTTTTGAAAAAAATCTTTGAGTTGTTTCTTTGAAACAAATTTTGTCTCTCTTGAGACAA
Found at i:33155 original size:89 final size:85
Alignment explanation
Indices: 32972--33155 Score: 206
Period size: 88 Copynumber: 2.1 Consensus size: 85
32962 GACAATTTCG
*
32972 TAAAAAATCTTTGAGTCTATTTATTTTGAAACAAAGTTTGTCTCTCTTGAAACAATTTCGTGAAA
1 TAAAAAATCTTTGAGTCTATTTATTTGGAAACAAAGTTTGTCTCTCTTGAAACAATTTCGTGAAA
*
33037 AAATATGTGAGTTGTTTCTT
66 AAATATGTGAGTTATTTCTT
* * * *
33057 TAGAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTT
1 T---AAAAAATCTTTGAGTCTATTTATTTGGAAAC-AAAGTTTGTCTCTCTTGAAACAATTTC--
* * * *
33122 TTGAAAATCATCTTTGAGTATATTTCTT
60 GTGAAAA-AATATGTGAGT-TATTTCTT
33150 TAAAAA
1 TAAAAA
33156 CAAATTTTGT
Statistics
Matches: 81, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
85 1 0.01
88 28 0.35
89 25 0.31
90 5 0.06
91 6 0.07
92 8 0.10
93 8 0.10
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (85 bp):
TAAAAAATCTTTGAGTCTATTTATTTGGAAACAAAGTTTGTCTCTCTTGAAACAATTTCGTGAAA
AAATATGTGAGTTATTTCTT
Found at i:33191 original size:64 final size:65
Alignment explanation
Indices: 33066--33192 Score: 166
Period size: 64 Copynumber: 2.0 Consensus size: 65
33056 TTAGAAAAAA
* * ** **
33066 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAAAATC
1 ATCTTTGAGTATATTTCTTTAAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAATGAAAATC
* * *
33131 ATCTTTGAGTATATTTCTTTAAAAAC-AAATTTTGTTTCTCTTGAGATAGTTTCTAATGAAAA
1 ATCTTTGAGTATATTTCTTTAAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAATGAAAA
33193 ATAACCTTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
64 31 0.58
65 22 0.42
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.45
Consensus pattern (65 bp):
ATCTTTGAGTATATTTCTTTAAAAACAAAATTTTGTCTCTCTTGAGACAATTTCTAATGAAAATC
Found at i:33399 original size:31 final size:31
Alignment explanation
Indices: 33364--33438 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
33354 CCTTGAGGCA
33364 GTTTCTCTAT-AAATACAAA-ATCTTTGAGTTT
1 GTTTCTCT-TGAAATA-AAACATCTTTGAGTTT
*
33395 GTTTCTCTTGAAATAAAACCATCTTTGAG-TC
1 GTTTCTCTTGAAATAAAA-CATCTTTGAGTTT
*
33426 GTTTCCCTTGAAA
1 GTTTCTCTTGAAA
33439 CAAATTTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 4 0.10
31 26 0.67
32 9 0.23
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (31 bp):
GTTTCTCTTGAAATAAAACATCTTTGAGTTT
Found at i:33714 original size:28 final size:28
Alignment explanation
Indices: 33668--33763 Score: 97
Period size: 28 Copynumber: 3.3 Consensus size: 28
33658 GAGACAGTTG
33668 CTTTTGAAACACATCATCTTTGAGTTTGTTT
1 CTTTTG-AA-ACA-CATCTTTGAGTTTGTTT
*
33699 -TTCTTGAAACGA-ATCTTTGGGTTTGTTT
1 CTT-TTGAAAC-ACATCTTTGAGTTTGTTT
* *
33727 CTTTTGAAGCACATCTTTGAGTTGGTTT
1 CTTTTGAAACACATCTTTGAGTTTGTTT
*
33755 CCTTTGAAA
1 CTTTTGAAA
33764 ACCATTATCT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
27 1 0.02
28 42 0.76
29 4 0.07
30 5 0.09
31 3 0.05
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (28 bp):
CTTTTGAAACACATCTTTGAGTTTGTTT
Found at i:34194 original size:3 final size:3
Alignment explanation
Indices: 34188--34231 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
34178 TTTTTTATAC
*
34188 TAT TAT TAGT TAT TAT T-T TAT TAT TAT TAT TAT CAT TAT TAT TA
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
34232 ATTAAATCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:36367 original size:15 final size:16
Alignment explanation
Indices: 36332--36362 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
36322 AATGCAGACC
36332 ATTTTTCTTTAAAATG
1 ATTTTTCTTTAAAATG
36348 ATTTTTCTTTAAAAT
1 ATTTTTCTTTAAAAT
36363 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTTCTTTAAAATG
Found at i:46501 original size:37 final size:36
Alignment explanation
Indices: 46451--46588 Score: 172
Period size: 37 Copynumber: 3.8 Consensus size: 36
46441 GTGCTTGTGG
* * * * *
46451 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATCT
* *
46488 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-CT
*
46525 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
46559 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
46589 GGACGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATCT
Found at i:46562 original size:34 final size:35
Alignment explanation
Indices: 46485--46585 Score: 161
Period size: 34 Copynumber: 2.9 Consensus size: 35
46475 TTAGTAGAAC
46485 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATG
1 TCTATCCTATTTTTAGGAGTTTGAATCCT---AAAATG
46523 T-TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
46556 TCTATCCTATTTTTAGGAGTTTGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
46586 GTAGGACGAA
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.53
37 27 0.44
38 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAATG
Found at i:47236 original size:105 final size:106
Alignment explanation
Indices: 47022--47477 Score: 637
Period size: 105 Copynumber: 4.3 Consensus size: 106
47012 CATTGTTCCA
* * *** *
47022 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCAGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * *
47087 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
47128 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
47192 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
47233 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAAG
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* *
47297 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
47338 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
* * * *
47403 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTCG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
47444 AGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTCGTGAAGTTGAAAT
47478 CGCGGATGGC
Statistics
Matches: 318, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
105 199 0.63
106 93 0.29
107 3 0.01
109 23 0.07
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:47374 original size:210 final size:212
Alignment explanation
Indices: 47022--47477 Score: 657
Period size: 211 Copynumber: 2.1 Consensus size: 212
47012 CATTGTTCCA
* *
47022 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCAGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAACCAGGAAATTGTTTGTTGACAAC
* *
47087 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTCGTGAAG
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTCGTGAAG
* * * *
47152 TTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
131 TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTT
* *
47216 GAACTTGCATTGTCTGG
196 GAACTTGCATTGCCTCG
* *** * *
47233 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTT-TTGACAAG
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAACCAGGAAATTGTTTGTTGACAAC
* *
47297 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GAAGTCCAATATCCTTCGTTGTGAA
66 CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCG-AGTCCAATATCCTTCGTCGTGAA
*
47361 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
130 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGT
**
47426 TGAACTTGTGTTGCCTCG
195 TGAACTTGCATTGCCTCG
*
47444 AGTGCCACGATATCCTCCGTTGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTCCGTTGTGAAGTTGAAAT
47478 CGCGGATGGC
Statistics
Matches: 217, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
209 1 0.00
210 93 0.43
211 97 0.45
212 3 0.01
214 23 0.11
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (212 bp):
AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAACCAGGAAATTGTTTGTTGACAAC
CAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGTCGTGAAG
TTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTT
GAACTTGCATTGCCTCG
Found at i:48212 original size:67 final size:65
Alignment explanation
Indices: 48081--48534 Score: 257
Period size: 65 Copynumber: 6.7 Consensus size: 65
48071 AAGATATCTG
* ** * * **
48081 TTGTTTCATGAGAAACGGACTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
48146 TT
64 TT
* *
48148 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
48213 T
65 T
* ** * ** *
48214 TTGTTTCAAGGGAAATTGTCTCAAGATAGACGAAATTTGTTTTAATAGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
* *
48279 ACAAA-ACT
57 TCAAAGATT
* * * * * * * * * * * *
48287 TAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * *
48352 TTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAG
1 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T--A-A-AT
*
48417 ACAAA-ATT
57 TCAAAGATT
* * * * * * * *** *
48425 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TT
1 TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
*
48489 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
1 T-TGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAA
48535 AAAAGCAATC
Statistics
Matches: 298, Mismatches: 67, Indels: 46
0.73 0.16 0.11
Matches are distributed among these distances:
64 11 0.04
65 122 0.41
66 4 0.01
67 24 0.08
68 31 0.10
70 1 0.00
72 2 0.01
73 93 0.31
74 10 0.03
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (65 bp):
TTGTTTCAAGAGAAATTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:48270 original size:36 final size:35
Alignment explanation
Indices: 48213--48469 Score: 179
Period size: 36 Copynumber: 7.3 Consensus size: 35
48203 ATTCAAAGAT
* * *
48213 TTTGTTTCAAGGGAAATTGTCTCAAGATAGACGAAA
1 TTTGTTTCAA-AGAAACTGTCTCAAGAGAGACGAAA
* *
48249 TTTGTTTTAATAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAA-AGAAACTGTCTCAAGAGAGACGAAA
* * * *
48285 CTTAGTTCCAAAAGCAACTGTCTCAAGGGAGACGAAA
1 -TTTGTTTC-AAAGAAACTGTCTCAAGAGAGACGAAA
* * *
48322 TTTGTTTCAAAGAAAACATAT-TC---A-A-A--TAT
1 TTTGTTTCAAAG-AAAC-TGTCTCAAGAGAGACGAAA
* * *
48351 TTTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAA-AGAAACTGTCTCAAGAGAGACGAAA
* * *
48387 TTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAA-AGAAACTGTCTCAAGAGAGACGAAA
* *
48423 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 -TTTGTTTCAA-AGAAACTGTCTCAAGAGAGACGAAA
*
48460 TTTATTTCAA
1 TTTGTTTCAA
48470 GGGAAATGTT
Statistics
Matches: 177, Mismatches: 30, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.01
29 16 0.09
30 1 0.01
31 1 0.01
32 2 0.01
33 1 0.01
34 1 0.01
35 4 0.02
36 85 0.48
37 62 0.35
38 2 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (35 bp):
TTTGTTTCAAAGAAACTGTCTCAAGAGAGACGAAA
Found at i:48323 original size:138 final size:138
Alignment explanation
Indices: 48165--48534 Score: 463
Period size: 138 Copynumber: 2.7 Consensus size: 138
48155 CAAGAGTAAT
* * * *
48165 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAAT
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAT
* * *
48230 TGTCTCAAGATAGACGAAATTTGTTTTAATAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
66 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
*
48295 AAAGCAAC
131 AAAGAAAC
* * * *
48303 TGTCTCAAGGGAGACGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGAAAT
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAT
* * * * * *
48368 TGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCA
66 TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
**
48433 AGGGAAAC
131 AAAGAAAC
* * * * * * *
48441 TATCTCAAGAGAGACGAAATTTATTTCAAGGGAAATGTTTTCAATG-TTTATGTTTCAAGAGAAA
1 TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTT-TGTTTCAAGGGAAA
* *
48505 CTGTCTCAAGGGAGACAAAATTTGTTTTAA
65 TTGTCTCAAGAGAGACAAAATTTGTTTTAA
48535 AAAAGCAATC
Statistics
Matches: 196, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
137 3 0.02
138 193 0.98
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (138 bp):
TGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAATATATTCAAAGATTTTGTTTCAAGGGAAAT
TGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCA
AAAGAAAC
Found at i:48475 original size:36 final size:36
Alignment explanation
Indices: 48355--48475 Score: 197
Period size: 36 Copynumber: 3.3 Consensus size: 36
48345 AAATATTTTG
*
48355 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
*
48391 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTA
* *
48428 TTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
48464 TTTCAAGGGAAA
1 TTTCAAGGGAAA
48476 TGTTTTCAAT
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
36 46 0.58
37 33 0.42
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:48924 original size:18 final size:18
Alignment explanation
Indices: 48897--48932 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
48887 TGTTGAATCC
* *
48897 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
48915 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
48933 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:49375 original size:22 final size:22
Alignment explanation
Indices: 49349--49397 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
49339 TTGTGTTTGG
* *
49349 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTGGATGC
*
49371 TCAAAGGTTTGATATTGGATGC
1 TCAAAGGTTTGACATTGGATGC
49393 TCAAA
1 TCAAA
49398 AGATTGATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGACATTGGATGC
Found at i:50065 original size:8 final size:7
Alignment explanation
Indices: 50053--50129 Score: 66
Period size: 8 Copynumber: 10.1 Consensus size: 7
50043 TGATTTTTGC
50053 TCTTTTT
1 TCTTTTT
50060 TCCTTTTGT
1 T-CTTTT-T
*
50069 TCTTGTT
1 TCTTTTT
50076 TCTCTTTT
1 TCT-TTTT
50084 TCTTTGTT
1 TCTTT-TT
50092 T-TTTTT
1 TCTTTTT
*
50098 TTTTTTT
1 TCTTTTT
50105 TGCTTTTT
1 T-CTTTTT
50113 TGCTTCTTT
1 T-CTT-TTT
50122 TCTTTTT
1 TCTTTTT
50129 T
1 T
50130 TGTTCTTGAT
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
6 3 0.05
7 20 0.33
8 31 0.52
9 6 0.10
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.79
Consensus pattern (7 bp):
TCTTTTT
Found at i:50066 original size:16 final size:17
Alignment explanation
Indices: 50047--50092 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
50037 TCTTTTTGAT
*
50047 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
50063 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
*
50080 TTTTTCT-TTGTTT
1 TTTTGCTCTTGTTT
50093 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:50100 original size:17 final size:18
Alignment explanation
Indices: 50080--50113 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50070 CTTGTTTCTC
50080 TTTTTCTTTG-TTTTTTT
1 TTTTTCTTTGCTTTTTTT
*
50097 TTTTTTTTTGCTTTTTT
1 TTTTTCTTTGCTTTTTT
50114 GCTTCTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (18 bp):
TTTTTCTTTGCTTTTTTT
Found at i:51935 original size:35 final size:35
Alignment explanation
Indices: 51889--51958 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
51879 TGTCCTCATT
51889 TTCTTTCTGAGCCCTTTTCGGACCATAGCCAGACC
1 TTCTTTCTGAGCCCTTTTCGGACCATAGCCAGACC
51924 TTCTTTCTGAGCCCTTTTCGGACCATAGCCAGACC
1 TTCTTTCTGAGCCCTTTTCGGACCATAGCCAGACC
51959 CCTGCGTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.31
Consensus pattern (35 bp):
TTCTTTCTGAGCCCTTTTCGGACCATAGCCAGACC
Found at i:53291 original size:2 final size:2
Alignment explanation
Indices: 53286--53343 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
53276 AAAAAGGAAA
53286 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
53328 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
53344 CAAGTATTAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53777 original size:2 final size:2
Alignment explanation
Indices: 53770--53796 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53760 TATTAAAGAA
53770 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 A
53797 ATAATAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54305 original size:37 final size:36
Alignment explanation
Indices: 54255--54392 Score: 163
Period size: 37 Copynumber: 3.8 Consensus size: 36
54245 GTGCCTGTGG
* * * * * *
54255 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA-AAATAT
* *
54292 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGTT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAAT-AT
*
54329 ATCCTATTTTTAGGAGTTTGAATCCTA--AAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATAT
54363 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTA
54393 GGACGAAAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
34 28 0.31
35 4 0.04
36 4 0.04
37 53 0.60
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATAT
Found at i:54366 original size:34 final size:34
Alignment explanation
Indices: 54291--54389 Score: 155
Period size: 34 Copynumber: 2.8 Consensus size: 34
54281 AGTAGAACTC
54291 TATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATGT
1 TATCCTATTTTTAGGAGTTTGAATCCT---AAAATGT
54328 TATCCTATTTTTAGGAGTTTGAATCCTAAAAT-T
1 TATCCTATTTTTAGGAGTTTGAATCCTAAAATGT
54361 ATATCCTATTTTTAGGAGTTTGAATCCTA
1 -TATCCTATTTTTAGGAGTTTGAATCCTA
54390 GTAGGACGAA
Statistics
Matches: 61, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
33 1 0.02
34 33 0.54
37 27 0.44
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (34 bp):
TATCCTATTTTTAGGAGTTTGAATCCTAAAATGT
Found at i:54473 original size:18 final size:18
Alignment explanation
Indices: 54452--54496 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
54442 CGACCGATGG
* *
54452 TGGTGTGATGGTCGGTGA
1 TGGTGCGATGGTCAGTGA
54470 TGGTGCGATGGTCAGTGA
1 TGGTGCGATGGTCAGTGA
54488 TGGTGCGAT
1 TGGTGCGAT
54497 AGAGATAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.09, G:0.47, T:0.31
Consensus pattern (18 bp):
TGGTGCGATGGTCAGTGA
Found at i:56014 original size:17 final size:18
Alignment explanation
Indices: 55992--56025 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
55982 ATAAAGTATA
55992 AAAATATAATA-ATAATG
1 AAAATATAATACATAATG
56009 AAAATATAATACATAAT
1 AAAATATAATACATAAT
56026 AATAGTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATATAATACATAATG
Found at i:57734 original size:105 final size:105
Alignment explanation
Indices: 57611--58586 Score: 1731
Period size: 105 Copynumber: 9.4 Consensus size: 105
57601 GTATTGTTCC
* * *
57611 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
*
57676 CAGCGGTCCCTTCGTCGTGAAGTTGAATTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
57716 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAAAGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
*
57781 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTGTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
57821 GAGTCCAATATCCTTCGTTGCGAATGTTGAAATTGGCTCTGAATTT-----A------TTGACAA
1 GAGTCCAATATCCTTCGTTGTGAA-GTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAA
* *
57875 CCAGTGGTCCCTTCGTCGTGAAGTCGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
57916 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
57981 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAAC-TTGCGTTGTCTG
58022 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
58087 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
58127 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
*
58192 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
58232 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
58297 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
58337 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
*
58402 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
58442 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
58507 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
58547 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
58587 GGTAAAACCT
Statistics
Matches: 841, Mismatches: 17, Indels: 26
0.95 0.02 0.03
Matches are distributed among these distances:
94 21 0.02
95 68 0.08
99 1 0.00
101 1 0.00
105 626 0.74
106 124 0.15
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTCGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:58787 original size:1 final size:1
Alignment explanation
Indices: 58781--58809 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
58771 TTGATGATGA
58781 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
58810 GAAGATGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:59401 original size:1 final size:1
Alignment explanation
Indices: 59395--59419 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
59385 ACCCTAAACG
59395 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
59420 CAACTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:70232 original size:17 final size:18
Alignment explanation
Indices: 70210--70243 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
70200 ATAAAGTATA
70210 AAAATATAATA-ATAATG
1 AAAATATAATACATAATG
70227 AAAATATAATACATAAT
1 AAAATATAATACATAAT
70244 AATAGTAGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATATAATACATAATG
Found at i:72289 original size:30 final size:27
Alignment explanation
Indices: 72232--72289 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 27
72222 CAAGAAACAT
**
72232 TATTATTTTATATATTTAATATTAATA
1 TATTATTTTATATATTTAATAAAAATA
72259 TATTATTTTAGTATCATTTTAATAAAAATA
1 TATTATTTTA-TAT-A-TTTAATAAAAATA
72289 T
1 T
72290 TAATTATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 10 0.38
28 3 0.12
29 1 0.04
30 12 0.46
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTATTTTATATATTTAATAAAAATA
Found at i:72378 original size:29 final size:29
Alignment explanation
Indices: 72346--72403 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
72336 TACTTTATTG
*
72346 TTATAATTATATTATTAA-AATATATAATA
1 TTATAATTATATT-TTAATAATACATAATA
* *
72375 TTATACTTTTATTTTAATAATACATAATA
1 TTATAATTATATTTTAATAATACATAATA
72404 AATTATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (29 bp):
TTATAATTATATTTTAATAATACATAATA
Found at i:73669 original size:13 final size:13
Alignment explanation
Indices: 73651--73675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73641 AGAAAGATTC
73651 AATTAAGAAAAAA
1 AATTAAGAAAAAA
73664 AATTAAGAAAAA
1 AATTAAGAAAAA
73676 CATAACAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (13 bp):
AATTAAGAAAAAA
Found at i:73822 original size:12 final size:12
Alignment explanation
Indices: 73801--73848 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
73791 TATACGGTAG
*
73801 AAAAATTAAATT
1 AAAAAATAAATT
73813 AAAAAATAAATTT
1 AAAAAATAAA-TT
*
73826 TAAAAATAAATGT
1 AAAAAATAAAT-T
*
73839 AAAAATTAAA
1 AAAAAATAAA
73849 CAAGTCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (12 bp):
AAAAAATAAATT
Found at i:73848 original size:13 final size:12
Alignment explanation
Indices: 73801--73848 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
73791 TATACGGTAG
73801 AAAAATTAAATT
1 AAAAATTAAATT
*
73813 AAAAAATAAATTTT
1 AAAAATTAAA--TT
73827 AAAAA-TAAATGT
1 AAAAATTAAAT-T
73839 AAAAATTAAA
1 AAAAATTAAA
73849 CAAGTCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 1 0.03
12 15 0.48
13 8 0.26
14 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (12 bp):
AAAAATTAAATT
Found at i:74109 original size:26 final size:26
Alignment explanation
Indices: 74080--74161 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
74070 GAATTTGGGA
*
74080 TATAATTCTTGAGGCAATTGTAATGT
1 TATAATTCTTGAGGCAGTTGTAATGT
74106 TATAATTCTTGAGGCAGTTGTAATGT
1 TATAATTCTTGAGGCAGTTGTAATGT
* *
74132 TATAATTCTTGAGACAGTAGTAATGT
1 TATAATTCTTGAGGCAGTTGTAATGT
74158 TATA
1 TATA
74162 CTTTATCCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (26 bp):
TATAATTCTTGAGGCAGTTGTAATGT
Found at i:76954 original size:21 final size:21
Alignment explanation
Indices: 76895--76968 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
76885 CACTGAGTGG
*
76895 CATATGAAGTTTGTCCCGAAGGA
1 CATATGAA--TTGTCCCAAAGGA
*
76918 CATGTGAATATGTCCCAAAGGA
1 CATATGAAT-TGTCCCAAAGGA
* * * *
76940 CTTATGAGTTGTCCCGATGGA
1 CATATGAATTGTCCCAAAGGA
*
76961 CCTATGAA
1 CATATGAA
76969 ACCCTCGACT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
21 17 0.41
22 17 0.41
23 7 0.17
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (21 bp):
CATATGAATTGTCCCAAAGGA
Found at i:84241 original size:21 final size:21
Alignment explanation
Indices: 84217--84258 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
84207 CACCGAGACT
84217 TGTTACATCAATATTCCGTTA
1 TGTTACATCAATATTCCGTTA
*
84238 TGTTACATCAATATTTCGTTA
1 TGTTACATCAATATTCCGTTA
84259 CTCTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.45
Consensus pattern (21 bp):
TGTTACATCAATATTCCGTTA
Found at i:84556 original size:36 final size:36
Alignment explanation
Indices: 84516--84588 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
84506 CTTCATTCTC
84516 GGCAATATTGAAGTAGCGGAGTTCATAAACATTCCG
1 GGCAATATTGAAGTAGCGGAGTTCATAAACATTCCG
84552 GGCAATATTGAAGTAGCGGAGTTCATAAACATTCCG
1 GGCAATATTGAAGTAGCGGAGTTCATAAACATTCCG
84588 G
1 G
84589 TCCTTGTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (36 bp):
GGCAATATTGAAGTAGCGGAGTTCATAAACATTCCG
Found at i:85844 original size:14 final size:14
Alignment explanation
Indices: 85825--85852 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
85815 CGACAATATT
85825 ACAAAAGGATTGGA
1 ACAAAAGGATTGGA
85839 ACAAAAGGATTGGA
1 ACAAAAGGATTGGA
85853 GAAGAATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.29, T:0.14
Consensus pattern (14 bp):
ACAAAAGGATTGGA
Found at i:85915 original size:18 final size:19
Alignment explanation
Indices: 85881--85917 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
85871 TTTGGTTCGT
85881 AAGATTACCGGTGAGAATAA
1 AAGATTACC-GTGAGAATAA
85901 AAGATTACC-TGAGAATA
1 AAGATTACCGTGAGAATA
85918 GGATTATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (19 bp):
AAGATTACCGTGAGAATAA
Found at i:95165 original size:28 final size:30
Alignment explanation
Indices: 95114--95173 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 30
95104 TTATTTATCA
95114 TAAAATTAATATTATTATTTTTTAAAATAT
1 TAAAATTAATATTATTATTTTTTAAAATAT
95144 TAAAA-TAAT-TTATT-TATTTTTAAAATAT
1 TAAAATTAATATTATTAT-TTTTTAAAATAT
95172 TA
1 TA
95174 TTTTTATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 1 0.03
28 19 0.66
29 4 0.14
30 5 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TAAAATTAATATTATTATTTTTTAAAATAT
Found at i:95326 original size:23 final size:23
Alignment explanation
Indices: 95277--95327 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
95267 GTGTTATATT
**
95277 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
95300 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
95323 ATATT
1 ATATT
95328 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:97801 original size:32 final size:32
Alignment explanation
Indices: 97760--97829 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
97750 AAAGTTTGAT
97760 CTTCATAAAGCTTTTGATACACTTAATTGGGA
1 CTTCATAAAGCTTTTGATACACTTAATTGGGA
97792 CTTCATAAAGCTTTTGATACACTTAATTGGGA
1 CTTCATAAAGCTTTTGATACACTTAATTGGGA
97824 CTTCAT
1 CTTCAT
97830 TTCTTCAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (32 bp):
CTTCATAAAGCTTTTGATACACTTAATTGGGA
Done.