Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006242.1 Hibiscus syriacus cultivar Beakdansim tig00014879_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: 78523
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:3739 original size:22 final size:22
Alignment explanation
Indices: 3711--3759 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3701 ACTTTTTTTT
* *
3711 GTCAAAGTTAATGGTTAGACCG
1 GTCAAAGTCAATGGTCAGACCG
3733 GTCAAAGTCAATGGTCAGACCG
1 GTCAAAGTCAATGGTCAGACCG
*
3755 ATCAA
1 GTCAA
3760 GGGTCGGGTT
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:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (22 bp):
GTCAAAGTCAATGGTCAGACCG
Found at i:6069 original size:103 final size:103
Alignment explanation
Indices: 5844--6061 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
5834 GTAGAGGGTC
*
5844 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
*
5909 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
5947 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATATGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
*
6012 TTGATCCTTGGCATATGTATATGATTTTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
6050 TATGTGGTCCTT
1 TATGTGGTCCTT
6062 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:6115 original size:23 final size:23
Alignment explanation
Indices: 6078--6140 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
6068 ATTATTATAT
*
6078 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
6101 GGTACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
**
6124 GGCACTTAGGTGCAATT
1 GGCACTCCGGTGCAATT
6141 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:12238 original size:20 final size:20
Alignment explanation
Indices: 12213--12250 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12203 GAATGCTAGA
*
12213 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
12233 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
12251 TAATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:12959 original size:103 final size:104
Alignment explanation
Indices: 12732--12951 Score: 397
Period size: 103 Copynumber: 2.1 Consensus size: 104
12722 GTAGAGGGTC
*
12732 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGTGAGGTCTGGTGAGACACAT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACA-GTGTGTGAGGTCTGGTGAGACACAT
*
12797 ACTTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
65 ACTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
12837 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACA-TGTGTGAGGTCTGGTGAGACACATA
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGTGTGTGAGGTCTGGTGAGACACATA
*
12901 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATTA
66 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
12940 TATGTGGTCCTT
1 TATGTGGTCCTT
12952 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
103 74 0.66
105 38 0.34
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (104 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGTGTGTGAGGTCTGGTGAGACACATA
CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:13001 original size:23 final size:23
Alignment explanation
Indices: 12968--13030 Score: 92
Period size: 23 Copynumber: 2.7 Consensus size: 23
12958 ATTATTATAT
12968 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
12991 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
13014 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
13031 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:16766 original size:6 final size:6
Alignment explanation
Indices: 16757--16789 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
16747 GAGAGAATTG
16757 GAATCT GAATCT GAATCT GAATCT GAATCT GAA
1 GAATCT GAATCT GAATCT GAATCT GAATCT GAA
16790 ACCTGTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (6 bp):
GAATCT
Found at i:17179 original size:5 final size:5
Alignment explanation
Indices: 17169--17194 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17159 ATAAAGTTTC
17169 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
17195 ATATATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:17420 original size:33 final size:28
Alignment explanation
Indices: 17375--17461 Score: 106
Period size: 26 Copynumber: 3.0 Consensus size: 28
17365 CCTAAACCCG
*
17375 ACTCGACCCGAATATCACACTTAAAAAA
1 ACTCGACTCGAATATCACACTTAAAAAA
17403 ACTCAACCCGACTCGAATATCACACTT-AAAAA
1 ACT-----CGACTCGAATATCACACTTAAAAAA
17435 ACT-GACTCGAATATCACACTTAAAAAA
1 ACTCGACTCGAATATCACACTTAAAAAA
17462 CCCGACCCGA
Statistics
Matches: 52, Mismatches: 1, Indels: 13
0.79 0.02 0.20
Matches are distributed among these distances:
26 18 0.35
27 5 0.10
28 3 0.06
32 8 0.15
33 18 0.35
ACGTcount: A:0.46, C:0.28, G:0.07, T:0.20
Consensus pattern (28 bp):
ACTCGACTCGAATATCACACTTAAAAAA
Found at i:17575 original size:27 final size:27
Alignment explanation
Indices: 17537--17588 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
17527 AAAACATGAC
* *
17537 CGACCCGAATATCACACTTAAAAAATT
1 CGACCCAAATATCAAACTTAAAAAATT
17564 CGACCCAAATATCAAACTTAAAAAA
1 CGACCCAAATATCAAACTTAAAAAA
17589 CCCGACTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (27 bp):
CGACCCAAATATCAAACTTAAAAAATT
Found at i:17594 original size:27 final size:27
Alignment explanation
Indices: 17536--17599 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
17526 AAAAACATGA
* * *
17536 CCGACCCGAATATCACACTTAAAAAAT
1 CCGACCCAAATATCAAACTTAAAAAAC
*
17563 TCGACCCAAATATCAAACTTAAAAAAC
1 CCGACCCAAATATCAAACTTAAAAAAC
*
17590 CCGACTCAAA
1 CCGACCCAAA
17600 CTCGGATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.47, C:0.30, G:0.06, T:0.17
Consensus pattern (27 bp):
CCGACCCAAATATCAAACTTAAAAAAC
Found at i:26833 original size:33 final size:35
Alignment explanation
Indices: 26764--26849 Score: 131
Period size: 33 Copynumber: 2.5 Consensus size: 35
26754 AATTCGTAGT
26764 TTATATCGATCATCAAACTAAGAGAGATTTAATGG
1 TTATATCGATCATCAAACTAAGAGAGATTTAATGG
*
26799 TTATATCGATCATCAAACT-A-AGAGATTTAGTGG
1 TTATATCGATCATCAAACTAAGAGAGATTTAATGG
* *
26832 TTATGTCAATCATCAAAC
1 TTATATCGATCATCAAAC
26850 GGGATTGTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
33 28 0.58
34 1 0.02
35 19 0.40
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (35 bp):
TTATATCGATCATCAAACTAAGAGAGATTTAATGG
Found at i:27604 original size:15 final size:15
Alignment explanation
Indices: 27586--27641 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
27576 TAACCGGTTT
27586 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
27601 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
27618 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
27633 CGATTTTAA
1 CGGTTTTAA
27642 TATTTCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:27614 original size:17 final size:17
Alignment explanation
Indices: 27589--27639 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
27579 CCGGTTTCGG
27589 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
27606 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
27621 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
27638 TT
1 TT
27640 AATATTTCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:27834 original size:21 final size:21
Alignment explanation
Indices: 27810--27862 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
27800 ACACTTAGGG
27810 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
27831 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
27852 TACCGATTCCC
1 AACCGATTCCC
27863 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:28079 original size:13 final size:13
Alignment explanation
Indices: 28058--28112 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
28048 AAGTTCGATA
*
28058 AATTCAAATACTT
1 AATTGAAATACTT
28071 AATTGAAATACTT
1 AATTGAAATACTT
* *
28084 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
28098 AATTGAAATACTT
1 AATTGAAATACTT
28111 AA
1 AA
28113 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:28143 original size:33 final size:33
Alignment explanation
Indices: 28098--28196 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
28088 AACTCAACAT
* *
28098 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
*
28131 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
28164 AATTCAAATACTTAAAAACTT-CAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
28196 A
1 A
28197 TTGAAACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 11 0.18
33 51 0.82
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTTGATA
Found at i:28215 original size:21 final size:21
Alignment explanation
Indices: 28191--28230 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
28181 ACTTCAAGTT
28191 TGATAATTGAAACAAAGTTTA
1 TGATAATTGAAACAAAGTTTA
*
28212 TGATAATTGAAATAAAGTT
1 TGATAATTGAAACAAAGTT
28231 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.35
Consensus pattern (21 bp):
TGATAATTGAAACAAAGTTTA
Found at i:30530 original size:16 final size:16
Alignment explanation
Indices: 30509--30540 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30499 TAAACCCAGA
*
30509 CCGGTTTTTTTTCCGG
1 CCGGTTTTTTATCCGG
30525 CCGGTTTTTTATCCGG
1 CCGGTTTTTTATCCGG
30541 TAAAAAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (16 bp):
CCGGTTTTTTATCCGG
Found at i:34906 original size:21 final size:21
Alignment explanation
Indices: 34884--34922 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
34874 ATGCCATATA
34884 AAAGATAG-GATT-TTGAGTTT
1 AAAGA-AGTGATTATTGAGTTT
34904 AAAGAAGTGATTATTGAGT
1 AAAGAAGTGATTATTGAGT
34923 AGAAACGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.12
20 9 0.53
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (21 bp):
AAAGAAGTGATTATTGAGTTT
Found at i:35001 original size:19 final size:20
Alignment explanation
Indices: 34966--35003 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34956 GAATATAAAA
*
34966 TGAGGTGAAATATGAAGTGT
1 TGAGCTGAAATATGAAGTGT
34986 TGAGCTGAAA-ATGAAGTG
1 TGAGCTGAAATATGAAGTG
35004 ATTTTTGTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.03, G:0.34, T:0.26
Consensus pattern (20 bp):
TGAGCTGAAATATGAAGTGT
Found at i:35208 original size:63 final size:63
Alignment explanation
Indices: 35086--35208 Score: 165
Period size: 63 Copynumber: 2.0 Consensus size: 63
35076 AAACGAAATA
* *
35086 AAAACATCGAATGCAATAAGTGCATCGATGCATAGGGAGTGCATCAATACACCCCTTAAGACG
1 AAAACATCGAATGCAATAAGTGCATCGATGCATAGAGAGTGCATCAATACACACCTTAAGACG
* ** * * * *
35149 AAAACATCGAATGTAATTTGTGTATCGATGCATAGATAGTGCATCGATACACACGTTAAG
1 AAAACATCGAATGCAATAAGTGCATCGATGCATAGAGAGTGCATCAATACACACCTTAAG
35209 GGATGCATCG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (63 bp):
AAAACATCGAATGCAATAAGTGCATCGATGCATAGAGAGTGCATCAATACACACCTTAAGACG
Found at i:35811 original size:18 final size:18
Alignment explanation
Indices: 35779--35831 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
35769 AGGGATTATC
* *
35779 AGTGGTCTTTTGGGACAT
1 AGTGGTCATTCGGGACAT
* *
35797 TGTGGTCATTCGGGATAT
1 AGTGGTCATTCGGGACAT
* *
35815 AGTGGTCCTTCAGGACA
1 AGTGGTCATTCGGGACA
35832 AATATTTAGT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.32, T:0.34
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:39521 original size:54 final size:54
Alignment explanation
Indices: 39463--39831 Score: 499
Period size: 54 Copynumber: 6.8 Consensus size: 54
39453 CCATACGGTC
* * * ** *
39463 ATTCATAAACATATTATGAATTATGTGGGTTGCACACATAGTGCCGAAAC-GATT
1 ATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAG-TT
* * ** **
39517 ATTCATCAACATACGATGAATTCCGTGAATTGCACACTTAGTGTTGAAATGGTT
1 ATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTT
* * *
39571 ATTCAACAACATATGATGGATTCTGTGAATTGAACACTTAGTGCCGAAACAGTT
1 ATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTT
* * * *
39625 ATTCATCAACATATAATGAATTCGGTGAATTGCACACTTAGTGTCGAAACGGTT
1 ATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTT
* * *
39679 ATTAATCAACATATGATGGATTCGGTGAATTGCACACTTAGTGCCGAAACAGTT
1 ATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTT
39733 ATTCATCAACATATGATGAATT-TCGTGAATTGCACACTTAGTGCCGAAACAGTT
1 ATTCATCAACATATGATGAATTCT-GTGAATTGCACACTTAGTGCCGAAACAGTT
*
39787 ATTCATCAACATATGATGAATTCCGTGAATTGCACACTTAGTGCC
1 ATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCC
39832 TATTTGGTAA
Statistics
Matches: 276, Mismatches: 36, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
54 275 1.00
55 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (54 bp):
ATTCATCAACATATGATGAATTCTGTGAATTGCACACTTAGTGCCGAAACAGTT
Found at i:40194 original size:22 final size:21
Alignment explanation
Indices: 40164--40222 Score: 86
Period size: 22 Copynumber: 2.9 Consensus size: 21
40154 TATGATACCC
*
40164 ATACCATGGTATCGATACTACT
1 ATACTATGGTATCGATACT-CT
40186 ATACTATGGTATCGATACTCT
1 ATACTATGGTATCGATACTCT
40207 A-A-TATGGTATCGATAC
1 ATACTATGGTATCGATAC
40223 CATTTTTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 14 0.39
20 1 0.03
21 3 0.08
22 18 0.50
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (21 bp):
ATACTATGGTATCGATACTCT
Found at i:41691 original size:42 final size:42
Alignment explanation
Indices: 41647--41845 Score: 149
Period size: 42 Copynumber: 4.7 Consensus size: 42
41637 AATTACACTC
* * * * **
41647 CTAATTTTTTAAATCTTATTTTTTACCTTTATAATTGATTTC-
1 CTAATTTTTTCAATC-CACTTTTTATCTTTATAATTGAAGTCT
* * *
41689 CTAATTTTATTCAATCACACTTTTTATCTTAATTATTAAAGTCT
1 CTAATTTT-TTCAATC-CACTTTTTATCTTTATAATTGAAGTCT
** *
41733 CTAATTTTTTTCAAT-CTTTTTTTATCTTTATAATTGAGGTCT
1 CTAA-TTTTTTCAATCCACTTTTTATCTTTATAATTGAAGTCT
* * *
41775 CTAATTTTTT-AATCCCACTTTTTAACTTTATAATTG-AGGCC
1 CTAATTTTTTCAAT-CCACTTTTTATCTTTATAATTGAAGTCT
41816 CTTAATTTTTT-AATCC-CATTTTCTATCTTT
1 C-TAATTTTTTCAATCCAC-TTTT-TATCTTT
41846 TCTACATATA
Statistics
Matches: 126, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
40 4 0.03
41 15 0.12
42 69 0.55
43 24 0.19
44 10 0.08
45 4 0.03
ACGTcount: A:0.26, C:0.16, G:0.04, T:0.55
Consensus pattern (42 bp):
CTAATTTTTTCAATCCACTTTTTATCTTTATAATTGAAGTCT
Found at i:41826 original size:43 final size:43
Alignment explanation
Indices: 41648--42168 Score: 277
Period size: 43 Copynumber: 12.0 Consensus size: 43
41638 ATTACACTCC
* * * * ***
41648 TAATTTTTTAAATCTTATTTTTTACCTTTATAATTGATTTCC-
1 TAATTTTTTTAATCTCACTTTTTAACTTTATAATTGAGGCCCT
* * * * * * * *
41690 TAATTTTATTCAATCACACTTTTTATCTTAATTATTAAAG-TCT
1 TAATTTT-TTTAATCTCACTTTTTAACTTTATAATTGAGGCCCT
* * *
41733 CTAATTTTTTTCAATCT--TTTTTTATCTTTATAATTGAGG-TCT
1 -TAATTTTTTT-AATCTCACTTTTTAACTTTATAATTGAGGCCCT
*
41775 CTAA-TTTTTTAATCCCACTTTTTAACTTTATAATTGAGGCCCT
1 -TAATTTTTTTAATCTCACTTTTTAACTTTATAATTGAGGCCCT
*
41818 TAA-TTTTTTAATCCCATTTTCTATCTTTTCT-ACATATATAATTGAGGCTCC-
1 TAATTTTTTTAAT--C----TC-A-CTTTT-TAAC-TTTATAATTGAGGC-CCT
* *
41869 TAA-TTTTTTAATCCCCAC-TTTTAAATTTATAA--GAGGCCCT
1 TAATTTTTTTAAT-CTCACTTTTTAACTTTATAATTGAGGCCCT
* * * * *
41909 TAAATTTTTTTTAATCTCGCTTTCTACCTTTACAATTGAGTCCC-
1 T-AA-TTTTTTTAATCTCACTTTTTAACTTTATAATTGAGGCCCT
* * * * *
41953 TAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACCCT
1 TAA-TTTTTTTAATCTCACTTTTTAACTTTATAATTGAGGCCCT
41997 TAA-TTTTTTAATCTCACCTTTTTAACTTTATAATTGAGGCCCT
1 TAATTTTTTTAATCTCA-CTTTTTAACTTTATAATTGAGGCCCT
* * * * * * *
42040 TGCATTTTTTCAATATCACTTTCTACCTTTATAATTGAGACCCC
1 T-AATTTTTTTAATCTCACTTTTTAACTTTATAATTGAGGCCCT
* * * *
42084 TAAGTTTTTTCAATCTCA-ATTAT-ACTTTTATAATTGAGGCCCC
1 TAA-TTTTTTTAATCTCACTTTTTAAC-TTTATAATTGAGGCCCT
* * *
42127 TAATTTTTTTCAATCTCAATTTCT-ACATTTATAATTAAGGCC
1 TAATTTTTTT-AATCTCACTTTTTAAC-TTTATAATTGAGGCC
42169 TCTATTTTTT
Statistics
Matches: 382, Mismatches: 63, Indels: 66
0.75 0.12 0.13
Matches are distributed among these distances:
39 2 0.01
40 10 0.03
41 8 0.02
42 93 0.24
43 138 0.36
44 73 0.19
45 18 0.05
46 1 0.00
48 1 0.00
49 1 0.00
50 9 0.02
51 26 0.07
52 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (43 bp):
TAATTTTTTTAATCTCACTTTTTAACTTTATAATTGAGGCCCT
Found at i:42070 original size:87 final size:86
Alignment explanation
Indices: 41915--42162 Score: 297
Period size: 87 Copynumber: 2.9 Consensus size: 86
41905 CCCTTAAATT
* * * * *
41915 TTTTTTAATCTCGCTTTCTACCTTTACAATTGAGTCCCTAAGTTTTTTCAATCTCAATTTCTACC
1 TTTTTTAATCTCACTTTATAACTTTATAATTGAGGCCCTAAGTTTTTTCAATCTCAATTTCTACC
*
41980 TTTATAATTGAGACCCTTAA-
66 TTTATAATTGAGACCCCTAAG
* * * *
42000 TTTTTTAATCTCACCTTTTTAACTTTATAATTGAGGCCCT-TGCATTTTTTCAATATCACTTTCT
1 TTTTTTAATCTCA-CTTTATAACTTTATAATTGAGGCCCTAAG--TTTTTTCAATCTCAATTTCT
42064 ACCTTTATAATTGAGACCCCTAAG
63 ACCTTTATAATTGAGACCCCTAAG
* *
42088 TTTTTTCAATCTCA-ATTAT-ACTTTTATAATTGAGGCCCCTAATTTTTTTCAATCTCAATTTCT
1 TTTTTT-AATCTCACTTTATAAC-TTTATAATTGAGG-CCCTAAGTTTTTTCAATCTCAATTTCT
*
42151 ACATTTATAATT
63 ACCTTTATAATT
42163 AAGGCCTCTA
Statistics
Matches: 139, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
85 13 0.09
86 24 0.17
87 85 0.61
88 10 0.07
89 7 0.05
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (86 bp):
TTTTTTAATCTCACTTTATAACTTTATAATTGAGGCCCTAAGTTTTTTCAATCTCAATTTCTACC
TTTATAATTGAGACCCCTAAG
Found at i:42118 original size:130 final size:129
Alignment explanation
Indices: 41854--42144 Score: 367
Period size: 130 Copynumber: 2.2 Consensus size: 129
41844 TTTCTACATA
41854 TATAATTGAGGCTCCTAATTTTTTAATC-C-CCACTTTTAAATTTATAAGAGGCCCTTAAATTTT
1 TATAATTGAGGC-CCTAATTTTTTAATCTCACCACTTTTAAATTTATAAGAGGCCCTTAAATTTT
* * * * *
41917 TTTTAATCTCGCTTTCTACCTTTACAATTGAGTCCCTAAGTTTTTTCAATCTCAATTTCTACCTT
65 TTTCAATATCACTTTCTACCTTTACAATTGAGCCCCTAAGTTTTTTCAATCTCAATTTATACCTT
* * * **
41982 TATAATTGAGACCCTTAATTTTTTAATCTCACC-TTTTTAACTTTATAATTGAGGCCCTTGCA-T
1 TATAATTGAGGCCC-TAATTTTTTAATCTCACCACTTTTAAATTTATAA--GAGGCCCTTAAATT
*
42045 TTTTTCAATATCACTTTCTACCTTTATAATTGAGACCCCTAAGTTTTTTCAATCTCAA-TTATAC
63 TTTTTCAATATCACTTTCTACCTTTACAATTGAG-CCCCTAAGTTTTTTCAATCTCAATTTATAC
*
42109 TTT
127 CTT
42112 TATAATTGAGGCCCCTAATTTTTTTCAATCTCA
1 TATAATTGAGG-CCCTAA-TTTTTT-AATCTCA
42145 ATTTCTACAT
Statistics
Matches: 141, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
127 2 0.01
128 24 0.17
129 14 0.10
130 53 0.38
131 41 0.29
132 7 0.05
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (129 bp):
TATAATTGAGGCCCTAATTTTTTAATCTCACCACTTTTAAATTTATAAGAGGCCCTTAAATTTTT
TTCAATATCACTTTCTACCTTTACAATTGAGCCCCTAAGTTTTTTCAATCTCAATTTATACCTT
Found at i:42168 original size:44 final size:43
Alignment explanation
Indices: 41844--42179 Score: 292
Period size: 43 Copynumber: 7.8 Consensus size: 43
41834 TTTTCTATCT
* * *
41844 TTTCTACATATATAATTGAGGCTCCTAATTTTTT-AATCCCCAC
1 TTTCTACATTTATAATTGAGGCCCCTAATTTTTTCAAT-CTCAC
* * * *
41887 TTT-TAAATTTATAA--GAGGCCCTTAAATTTTTTTTAATCTCGC
1 TTTCTACATTTATAATTGAGGCCCCT-AA-TTTTTTCAATCTCAC
* * * *
41929 TTTCTACCTTTACAATTGA-GTCCCTAAGTTTTTTCAATCTCAA
1 TTTCTACATTTATAATTGAGGCCCCTAA-TTTTTTCAATCTCAC
* * *
41972 TTTCTACCTTTATAATTGAGACCCTTAATTTTTT-AATCTCACC
1 TTTCTACATTTATAATTGAGGCCCCTAATTTTTTCAATCTCA-C
* * * *
42015 TTTTTA-ACTTTATAATTGAGGCCCTTGCATTTTTTCAATATCAC
1 TTTCTACA-TTTATAATTGAGGCCCCT-AATTTTTTCAATCTCAC
* *
42059 TTTCTACCTTTATAATTGAGACCCCTAAGTTTTTTCAATCTCA-
1 TTTCTACATTTATAATTGAGGCCCCTAA-TTTTTTCAATCTCAC
* * * *
42102 ATTATACTTTTATAATTGAGGCCCCTAATTTTTTTCAATCTCAA
1 TTTCTACATTTATAATTGAGGCCCCTAA-TTTTTTCAATCTCAC
* * *
42146 TTTCTACATTTATAATTAAGGCCTCTATTTTTTT
1 TTTCTACATTTATAATTGAGGCCCCTAATTTTTT
42180 TTCAATTTCA
Statistics
Matches: 237, Mismatches: 42, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
40 7 0.03
41 2 0.01
42 28 0.12
43 119 0.50
44 73 0.31
45 8 0.03
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.46
Consensus pattern (43 bp):
TTTCTACATTTATAATTGAGGCCCCTAATTTTTTCAATCTCAC
Found at i:42179 original size:87 final size:86
Alignment explanation
Indices: 41854--42185 Score: 261
Period size: 87 Copynumber: 3.8 Consensus size: 86
41844 TTTCTACATA
* * * ** * *
41854 TATAATTGAGGCTCCTAATTTTTT-AATCCCCACTTT-TAAATTTATAA--GAGGCCCTTAAATT
1 TATAATTGAGGCCCCTAATTTTTTCAAT-CTCAATTTCTACCTTTATAATTGAGACCC-TATA-T
* * * * *
41915 TTTTTTAATCTCGCTTTCTACCTT
63 TTTTTCAATCTCACATTATAACTT
* *
41939 TACAATTGA-GTCCCTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACCCT-TAATT
1 TATAATTGAGGCCCCTAA-TTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACCCTAT-ATT
* *
42002 TTTT-AATCTCACCTTTTTAACTT
64 TTTTCAATCTCA-CATTATAACTT
* * * *
42025 TATAATTGAGGCCCTTGCATTTTTTCAATATCACTTTCTACCTTTATAATTGAGACCCCTA-AGT
1 TATAATTGAGGCCCCT-AATTTTTTCAATCTCAATTTCTACCTTTATAATTGAGA-CCCTATA-T
42089 TTTTTCAATCTCA-ATTAT-ACTTT
63 TTTTTCAATCTCACATTATAAC-TT
* * * *
42112 TATAATTGAGGCCCCTAATTTTTTTCAATCTCAATTTCTACATTTATAATTAAGGCCTCTATTTT
1 TATAATTGAGGCCCCTAA-TTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACC-CTA-TAT
42177 TTTTTCAAT
63 TTTTTCAAT
42186 TTCATAAAAT
Statistics
Matches: 201, Mismatches: 28, Indels: 33
0.77 0.11 0.13
Matches are distributed among these distances:
84 6 0.03
85 26 0.13
86 40 0.20
87 95 0.47
88 27 0.13
89 7 0.03
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (86 bp):
TATAATTGAGGCCCCTAATTTTTTCAATCTCAATTTCTACCTTTATAATTGAGACCCTATATTTT
TTCAATCTCACATTATAACTT
Found at i:42738 original size:21 final size:19
Alignment explanation
Indices: 42712--42767 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 19
42702 CATATTCGCA
42712 TTGCGATAGTCCAAGTTTGCG
1 TTGCGATAGTCCAAG-TT-CG
*
42733 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TAGTCCAAGTTCG
42754 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
42768 AATCGCAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
19 7 0.23
21 14 0.45
22 2 0.06
23 8 0.26
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (19 bp):
TTGCGATAGTCCAAGTTCG
Found at i:42870 original size:12 final size:11
Alignment explanation
Indices: 42853--42888 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
42843 GACACGTATT
42853 ACCACGACCACG
1 ACCACGACC-CG
42865 ACCACGACCCG
1 ACCACGACCCG
42876 ACC-CGACCCG
1 ACCACGACCCG
42886 ACC
1 ACC
42889 CGAGACGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.28, C:0.56, G:0.17, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:42879 original size:5 final size:5
Alignment explanation
Indices: 42857--42891 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
42847 CGTATTACCA
42857 CGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
42892 GACGAGACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:42947 original size:21 final size:21
Alignment explanation
Indices: 42921--42987 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
42911 GCGGCGGCGC
42921 GCGATAGTCCAAGTTCGCATT
1 GCGATAGTCCAAGTTCGCATT
42942 GCGATAGTCCAAGTTCGCATT
1 GCGATAGTCCAAGTTCGCATT
* *
42963 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCCAAGTTCGCATT
42984 GCGA
1 GCGA
42988 ATCTAGAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (21 bp):
GCGATAGTCCAAGTTCGCATT
Found at i:44162 original size:2 final size:2
Alignment explanation
Indices: 44155--44180 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44145 CTAGCCCACC
44155 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
44181 TAAATAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46070 original size:21 final size:20
Alignment explanation
Indices: 45984--46141 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
45974 AAATGACCAA
**
45984 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
46003 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
46023 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
46043 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
46064 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
46085 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
46105 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
46126 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
46142 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:46173 original size:20 final size:20
Alignment explanation
Indices: 46108--46357 Score: 229
Period size: 20 Copynumber: 12.5 Consensus size: 20
46098 CGATTTTCCA
* ** *
46108 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
46128 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
46148 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
46168 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
46188 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
46208 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
46228 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
46248 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
46268 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
46288 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
46308 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
46328 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
46348 AAATCACAAC
1 AAATCGCAAC
46358 ACTGAAATTT
Statistics
Matches: 195, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
20 194 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:47075 original size:24 final size:24
Alignment explanation
Indices: 47036--47082 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47026 AAATTTGGTC
47036 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
47060 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
47083 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:49649 original size:19 final size:19
Alignment explanation
Indices: 49590--49705 Score: 128
Period size: 19 Copynumber: 6.6 Consensus size: 19
49580 GAAATGAAAA
49590 TCGCATTGCGA--TTC-TT
1 TCGCATTGCGATTTTCATT
49606 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
49623 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
49643 TCGCATTGCGA---TC-TC
1 TCGCATTGCGATTTTCATT
49658 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
49675 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
49694 TCGCATTGCGAT
1 TCGCATTGCGAT
49706 AGTCAATTTT
Statistics
Matches: 84, Mismatches: 4, Indels: 21
0.77 0.04 0.19
Matches are distributed among these distances:
13 6 0.07
14 6 0.07
15 4 0.05
16 10 0.12
17 6 0.07
18 2 0.02
19 35 0.42
20 15 0.18
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:49694 original size:51 final size:52
Alignment explanation
Indices: 49590--49705 Score: 198
Period size: 51 Copynumber: 2.2 Consensus size: 52
49580 GAAATGAAAA
*
49590 TCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
49643 TCGCATTGCGATCTCTCGTTGCGATTTTCATTT-TGCATTGCGATTTTCATT
1 TCGCATTGCGATCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
49694 TCGCATTGCGAT
1 TCGCATTGCGAT
49706 AGTCAATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 29 0.48
52 21 0.34
53 11 0.18
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:49816 original size:33 final size:33
Alignment explanation
Indices: 49764--49925 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 33
49754 CCATTACATT
49764 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
* *
49798 TCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
* * * *
49830 T-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAGAA
49869 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
*
49902 TCGCAATGCGAAATTAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
49926 TTGCGATTCT
Statistics
Matches: 105, Mismatches: 12, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 54 0.51
34 10 0.10
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:49820 original size:19 final size:19
Alignment explanation
Indices: 49764--49931 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
49754 CCATTACATT
49764 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
49784 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
49798 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
49817 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
49836 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
49850 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
49869 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
49888 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
49902 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
49921 TCGCATTGCGA
1 TCGCAATGCGA
49932 TTCTCCCATT
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.24
15 3 0.02
16 6 0.05
17 5 0.04
18 4 0.03
19 71 0.57
20 6 0.05
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:49843 original size:52 final size:52
Alignment explanation
Indices: 49764--49931 Score: 309
Period size: 52 Copynumber: 3.2 Consensus size: 52
49754 CCATTACATT
49764 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
49817 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
49869 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
49921 TCGCATTGCGA
1 TCGCAATGCGA
49932 TTCTCCCATT
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 104 0.92
53 9 0.08
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:49980 original size:19 final size:19
Alignment explanation
Indices: 49938--50037 Score: 129
Period size: 19 Copynumber: 5.5 Consensus size: 19
49928 GCGATTCTCC
49938 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
*
49958 CATTGCGATTTGCATTTCG
1 CATTGCGATTTTCATTTCG
*
49977 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
49993 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
50010 CATTGCGATTTTTATTTCG
1 CATTGCGATTTTCATTTCG
50029 CATTGCGAT
1 CATTGCGAT
50038 AGTCAATTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 6 0.09
19 35 0.50
20 16 0.23
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:50034 original size:52 final size:53
Alignment explanation
Indices: 49921--50037 Score: 191
Period size: 53 Copynumber: 2.2 Consensus size: 53
49911 GAAATTAAAA
49921 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTGCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTGCATT
* * **
49974 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTTATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTGCATT
50026 TCGCATTGCGAT
1 TCGCATTGCGAT
50038 AGTCAATTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 28 0.47
53 32 0.53
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTGCATT
Found at i:50163 original size:14 final size:14
Alignment explanation
Indices: 50144--50180 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
50134 CATCAATTAC
50144 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
50158 ACAAATCATCTTTT
1 ACAAATCAACTTTT
50172 ACAAATCAA
1 ACAAATCAA
50181 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:52125 original size:19 final size:18
Alignment explanation
Indices: 52096--52195 Score: 67
Period size: 19 Copynumber: 5.9 Consensus size: 18
52086 GAAAGTTTAC
52096 TTTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
52113 TTTCGCATTGCGA--TTC-
1 TTTCGC-TTGCGATTTTCA
*
52129 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGATTTTCA
52146 TTTCGCGTTGCGA---TC-
1 TTTCGC-TTGCGATTTTCA
**
52161 TTGTCG-TTGCGATTTTGG
1 TT-TCGCTTGCGATTTTCA
52179 TTTCGCGTTGCGATTTT
1 TTTCGC-TTGCGATTTT
52196 AAGTTTCGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 26
0.69 0.03 0.27
Matches are distributed among these distances:
14 12 0.18
15 2 0.03
16 12 0.18
17 16 0.24
18 2 0.03
19 22 0.33
ACGTcount: A:0.09, C:0.19, G:0.24, T:0.48
Consensus pattern (18 bp):
TTTCGCTTGCGATTTTCA
Found at i:52135 original size:33 final size:34
Alignment explanation
Indices: 52098--52193 Score: 151
Period size: 33 Copynumber: 2.9 Consensus size: 34
52088 AAGTTTACTT
*
52098 TCGTTGCGATTTTCATTTCGCATTGCGATTC-TG
1 TCGTTGCGATTTTCATTTCGCGTTGCGATTCTTG
52131 TCGTTGCGATTTTCATTTCGCGTTGCGA-TCTTG
1 TCGTTGCGATTTTCATTTCGCGTTGCGATTCTTG
**
52164 TCGTTGCGATTTTGGTTTCGCGTTGCGATT
1 TCGTTGCGATTTTCATTTCGCGTTGCGATT
52194 TTAAGTTTCG
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
32 2 0.03
33 55 0.95
34 1 0.02
ACGTcount: A:0.09, C:0.20, G:0.25, T:0.46
Consensus pattern (34 bp):
TCGTTGCGATTTTCATTTCGCGTTGCGATTCTTG
Found at i:52203 original size:20 final size:19
Alignment explanation
Indices: 52132--52211 Score: 73
Period size: 19 Copynumber: 4.4 Consensus size: 19
52122 GCGATTCTGT
52132 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
52151 CGTTGCGATCTT-G--T--
1 CGTTGCGATTTTAGTTTCG
*
52165 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
52184 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
52204 TGTTGCGA
1 CGTTGCGA
52212 AAGTAAACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
14 11 0.22
15 1 0.02
16 1 0.02
17 1 0.02
19 23 0.46
20 13 0.26
ACGTcount: A:0.10, C:0.17, G:0.28, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:52409 original size:93 final size:93
Alignment explanation
Indices: 52250--52630 Score: 744
Period size: 93 Copynumber: 4.1 Consensus size: 93
52240 TTGAATGGAT
52250 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
52315 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
52343 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
52408 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
52436 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
52501 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
52529 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
52594 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
52622 AAATTTACT
1 AAATTTACT
52631 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 285 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:54352 original size:14 final size:14
Alignment explanation
Indices: 54333--54422 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
54323 TTGAAATGAA
54333 AATCGCAACGAGAG
1 AATCGCAACGAGAG
54347 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
54364 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
54380 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
54399 AATCGCAACGAGAG
1 AATCGCAACGAGAG
54413 AATCGCAACG
1 AATCGCAACG
54423 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:54370 original size:33 final size:33
Alignment explanation
Indices: 54325--54439 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
54315 TCTTTTGGTT
54325 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
54358 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
54391 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
54424 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
54440 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:54371 original size:19 final size:18
Alignment explanation
Indices: 54332--54444 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
54322 GTTGAAATGA
54332 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
54347 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
54364 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
54380 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
54397 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
54413 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
54430 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
54445 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:54475 original size:14 final size:14
Alignment explanation
Indices: 54456--54512 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
54446 TTTGGTTTCG
54456 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
54470 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
54489 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
54503 CGTTGCGATT
1 CGTTGCGATT
54513 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:54488 original size:33 final size:33
Alignment explanation
Indices: 54440--54520 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
54430 AAAATCGCAA
**
54440 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
54473 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
54506 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
54521 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:54523 original size:21 final size:21
Alignment explanation
Indices: 54497--54572 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
54487 CGCGTTGCGA
54497 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
54518 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
54538 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
54559 TTTTCTCGTTGCGA
1 TTCTCTCGTTGCGA
54573 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:54553 original size:41 final size:41
Alignment explanation
Indices: 54496--54573 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
54486 TCGCGTTGCG
54496 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
* *
54537 ATTCTCTCGTTGCGATTTTCATTTTTCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGAC
54574 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.26, G:0.18, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
Found at i:54699 original size:33 final size:33
Alignment explanation
Indices: 54652--54722 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
54642 AATACTAACT
* *
54652 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
54685 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
54718 TGAAA
1 TGAAA
54723 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:54956 original size:22 final size:22
Alignment explanation
Indices: 54904--54958 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
54894 TGGTTGTGAG
**
54904 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
54926 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
54948 GGATTTCTTCG
1 GGATTTCTTCG
54959 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:55124 original size:39 final size:40
Alignment explanation
Indices: 55081--55198 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 40
55071 TACGCGTAGC
*
55081 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
55120 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
** * * * *
55160 GATTATCGTTGCGATTTACGGATACGCATTGCGATTTAC
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTAC
55199 CCATACGCGT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 14 0.21
40 52 0.76
41 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:55297 original size:20 final size:20
Alignment explanation
Indices: 55103--55296 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
55093 GCTTTAAATA
55103 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
** *
55123 TATCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTACGGAT
*
55143 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
**
55163 TATCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
* * **
55183 ACGCATTGCGATTTACCCAT
1 TCGCGTTGCGATTTACGGAT
*
55203 ACGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
* *
55223 ACACGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACGGAT
* *
55243 ACGCGTTGCGATTTATGTG-T
1 TCGCGTTGCGATTTACG-GAT
* **
55263 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACGGAT
55283 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
55297 TGGAAAATCG
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGGAT
Found at i:55313 original size:21 final size:21
Alignment explanation
Indices: 55283--55365 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
55273 ATTTTCATAT
*
55283 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
55304 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
55325 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
55346 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
55366 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:55356 original size:42 final size:43
Alignment explanation
Indices: 55263--55361 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
55253 ATTTATGTGT
* *
55263 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
55304 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
55346 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
55362 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:55541 original size:21 final size:19
Alignment explanation
Indices: 55517--55561 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
55507 AAAAATGCAG
*
55517 AATAAAAATAAGTAGAAAAA
1 AATAAAAATAA-AAGAAAAA
55537 AA-ATAAAATAAAAGAAAAA
1 AATA-AAAATAAAAGAAAAA
55556 AATAAA
1 AATAAA
55562 TAAATAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (19 bp):
AATAAAAATAAAAGAAAAA
Found at i:55585 original size:2 final size:2
Alignment explanation
Indices: 55578--55602 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55568 AAGAAATGAA
55578 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 A
55603 ATAAAAAATG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55818 original size:2 final size:2
Alignment explanation
Indices: 55813--55841 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55803 GAAAATACAC
55813 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55842 AATGAGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55981 original size:2 final size:2
Alignment explanation
Indices: 55938--55966 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
55928 ATATAATCAA
55938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55967 ATAATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57576 original size:106 final size:106
Alignment explanation
Indices: 57431--58158 Score: 1255
Period size: 106 Copynumber: 6.9 Consensus size: 106
57421 AACTGGGAAA
* * *
57431 TTGTTTATTGACAACCGGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
57496 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
* *
57537 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTAAAGTTGAACTTACGTTGTCTGGAGTCCAATA
1 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
57602 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
*
57643 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATA
1 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* * *
57708 TCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
*
57749 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
**
57814 TTATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
* *
57854 ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATA
1 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
* *
57919 TCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
* *
57959 ATGTTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
58024 TCCTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAG
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
58065 -TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
1 TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
*
58129 TCCTTCGTTGTGAAGTTGAAATTGACTCTG
66 TCCTTCGTTGTGAAGTTGAAATTGGCTCTG
58159 GGTAAAACCT
Statistics
Matches: 591, Mismatches: 30, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
105 291 0.49
106 300 0.51
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
TTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
TCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAG
Found at i:58931 original size:21 final size:23
Alignment explanation
Indices: 58907--58955 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
58897 ACCCCCCTTA
58907 TTTTCTCTTCTT-TTGTTCTTTTT
1 TTTTCTCTTCTTCTTGTTC-TTTT
* *
58930 TTTTCTCTTTTTCTTTTTCTTTT
1 TTTTCTCTTCTTCTTGTTCTTTT
58953 TTT
1 TTT
58956 AATTTAGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (23 bp):
TTTTCTCTTCTTCTTGTTCTTTT
Found at i:58935 original size:18 final size:19
Alignment explanation
Indices: 58907--58952 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
58897 ACCCCCCTTA
*
58907 TTTTCTCTTCT-TTTGTTCT
1 TTTTCTTTTCTCTTT-TTCT
58926 TTTT-TTTTCTCTTTTTCT
1 TTTTCTTTTCTCTTTTTCT
58944 TTTTCTTTT
1 TTTTCTTTT
58953 TTTAATTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTCTTTTCTCTTTTTCT
Found at i:58936 original size:23 final size:24
Alignment explanation
Indices: 58907--58955 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
58897 ACCCCCCTTA
58907 TTTTCTCTTCTT-TTGTTCTTTTT
1 TTTTCTCTTCTTCTTGTTCTTTTT
* *
58930 TTTTCTCTTTTTCTTTTTCTTTTT
1 TTTTCTCTTCTTCTTGTTCTTTTT
58954 TT
1 TT
58956 AATTTAGGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (24 bp):
TTTTCTCTTCTTCTTGTTCTTTTT
Found at i:58938 original size:12 final size:11
Alignment explanation
Indices: 58907--58955 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
58897 ACCCCCCTTA
* *
58907 TTTTCTCTTCT
1 TTTTTTCTTTT
*
58918 TTTGTTCTTTT
1 TTTTTTCTTTT
58929 TTTTTCTCTTTT
1 TTTTT-TCTTTT
58941 TCTTTTTCTTTT
1 T-TTTTTCTTTT
58953 TTT
1 TTT
58956 AATTTAGGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 14 0.44
12 14 0.44
13 4 0.12
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:59011 original size:8 final size:8
Alignment explanation
Indices: 59000--59044 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
58990 CGTTTTTCTC
59000 TTTTTGTT
1 TTTTTGTT
*
59008 TTTTTGCT
1 TTTTTGTT
*
59016 CTTTTGTT
1 TTTTTGTT
59024 TTTTTGTT
1 TTTTTGTT
*
59032 TTCTTGTT
1 TTTTTGTT
59040 TTTTT
1 TTTTT
59045 TTCAACTTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.82
Consensus pattern (8 bp):
TTTTTGTT
Found at i:59017 original size:17 final size:17
Alignment explanation
Indices: 58992--59044 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 17
58982 ACCCTAAACG
58992 TTTTT-CTCTTTTTGTT
1 TTTTTGCTCTTTTTGTT
59008 TTTTTGCTC-TTTTGTT
1 TTTTTGCTCTTTTTGTT
59024 TTTTTG-T-TTTCTTGTT
1 TTTTTGCTCTTT-TTGTT
59040 TTTTT
1 TTTTT
59045 TTCAACTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.09
16 28 0.82
17 3 0.09
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.81
Consensus pattern (17 bp):
TTTTTGCTCTTTTTGTT
Found at i:65821 original size:39 final size:39
Alignment explanation
Indices: 65754--65831 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
65744 TTCACAGCAG
* *
65754 GTGCAACTTTCGCTTTGGTAACGAATGAGTCCTCGGGTA
1 GTGCAACTTTCCCTTTAGTAACGAATGAGTCCTCGGGTA
* *
65793 GTGCAACTTTCCCTTTAGTAGCGGATGAGTCCTCGGGTA
1 GTGCAACTTTCCCTTTAGTAACGAATGAGTCCTCGGGTA
65832 ATACTCCGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (39 bp):
GTGCAACTTTCCCTTTAGTAACGAATGAGTCCTCGGGTA
Found at i:66198 original size:22 final size:21
Alignment explanation
Indices: 66174--66216 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 21
66164 ATACGAATGT
66174 AAAAACATGGAGAATAAAAAATAA
1 AAAAACAT-GA-AATAAAAAAT-A
66198 AAAAACATGAAATAAAAAA
1 AAAAACATGAAATAAAAAA
66217 ATACAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (21 bp):
AAAAACATGAAATAAAAAATA
Found at i:69501 original size:2 final size:2
Alignment explanation
Indices: 69494--69520 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
69484 GAAATATAAA
69494 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
69521 AAATAAAAAA
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:69853 original size:12 final size:10
Alignment explanation
Indices: 69836--69902 Score: 56
Period size: 9 Copynumber: 7.0 Consensus size: 10
69826 ATAAAATAGA
69836 AAAT-ATAAT
1 AAATAATAAT
69845 CAAAT-ATATAT
1 -AAATAATA-AT
69856 ATAATAATAAT
1 A-AATAATAAT
69867 -AATAATAAT
1 AAATAATAAT
69876 -AATAATAAT
1 AAATAATAAT
69885 -AATAA-AAT
1 AAATAATAAT
*
69893 ATATAATAAT
1 AAATAATAAT
69903 GAAACGTAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
8 3 0.06
9 27 0.53
10 11 0.22
11 7 0.14
12 3 0.06
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATAATAAT
Found at i:69864 original size:3 final size:3
Alignment explanation
Indices: 69856--69902 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
69846 AAATATATAT
69856 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
69901 AT
1 AT
69903 GAAACGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:77152 original size:26 final size:26
Alignment explanation
Indices: 77123--77187 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
77113 TTATCAATAT
77123 ATATTTATTATTAA-CTTAATTTAAAA
1 ATATTTATT-TTAATCTTAATTTAAAA
*
77149 ATATTATATTTTAATTTTAATTTAAAA
1 ATATT-TATTTTAATCTTAATTTAAAA
*
77176 ATATATATTTTA
1 ATATTTATTTTA
77188 TTTTTCTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 16 0.46
27 19 0.54
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
ATATTTATTTTAATCTTAATTTAAAA
Found at i:77184 original size:31 final size:27
Alignment explanation
Indices: 77118--77191 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 27
77108 TAACGTTATC
77118 AATATATATTTATTATTAACTTAATTTA
1 AATATATATTTATT-TTAACTTAATTTA
*
77146 AA-A-ATATTATATTTTAATTTTAATTTAAA
1 AATATATATT-TATTTTAA-CTTAATTT--A
77175 AATATATATTTTATTTT
1 AATATATA-TTTATTTT
77192 TCTAAACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
26 9 0.24
27 12 0.32
28 2 0.05
29 3 0.08
30 1 0.03
31 9 0.24
32 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (27 bp):
AATATATATTTATTTTAACTTAATTTA
Found at i:77192 original size:26 final size:27
Alignment explanation
Indices: 77138--77192 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
77128 TATTATTAAC
77138 TTAATTTAAAAATATTATATTTTAATT
1 TTAATTTAAAAATATTATATTTTAATT
*
77165 TTAATTTAAAAATA-TATATTTTATTT
1 TTAATTTAAAAATATTATATTTTAATT
77191 TT
1 TT
77193 CTAAACTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTAATTTAAAAATATTATATTTTAATT
Found at i:77605 original size:24 final size:25
Alignment explanation
Indices: 77578--77646 Score: 61
Period size: 26 Copynumber: 2.7 Consensus size: 25
77568 TAAAAGTATT
* *
77578 TTAACATAAAATATATATATT-AAA
1 TTAAAATAAAATAAATATATTGAAA
*
77602 TTAAAATAGAAAATAAATATTTTGAAA
1 TTAAAAT--AAAATAAATATATTGAAA
*
77629 TTAATATAATAA-AAATAT
1 TTAAAATAA-AATAAATAT
77647 TTAATCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
24 6 0.16
25 8 0.22
26 14 0.38
27 9 0.24
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (25 bp):
TTAAAATAAAATAAATATATTGAAA
Found at i:78199 original size:31 final size:30
Alignment explanation
Indices: 78155--78220 Score: 114
Period size: 31 Copynumber: 2.2 Consensus size: 30
78145 AATGAGAAAA
*
78155 ATGTACAAACACAAACATAAATGATCAATC
1 ATGTACAAACACAAACATAAACGATCAATC
78185 ATGTACAAAACACAAACATAAACGATCAATC
1 ATGTAC-AAACACAAACATAAACGATCAATC
78216 ATGTA
1 ATGTA
78221 GGAAATAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 6 0.18
31 28 0.82
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.20
Consensus pattern (30 bp):
ATGTACAAACACAAACATAAACGATCAATC
Done.