Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002238.1 Hibiscus syriacus cultivar Beakdansim tig00004552_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: 67401
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:319 original size:43 final size:43
Alignment explanation
Indices: 193--307 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
183 ATATAAGGGT
* *
193 TTCAATAATG-ATATAAGGTTTTCGATACCGATCGTTTTGGAT
1 TTCAATAATGAATATAAGGTTTTCGATACTGATCGTTTTGGAG
* * * *
235 TTCGATAATGAATA-CATGTCTTTCGATAGTGATCGTTTTGGAG
1 TTCAATAATGAATATAAGGT-TTTCGATACTGATCGTTTTGGAG
*
278 TTCAATGATGAATATAAGGTTTTCGATACT
1 TTCAATAATGAATATAAGGTTTTCGATACT
308 AACCATTTTG
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
42 12 0.20
43 44 0.75
44 3 0.05
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (43 bp):
TTCAATAATGAATATAAGGTTTTCGATACTGATCGTTTTGGAG
Found at i:1904 original size:25 final size:24
Alignment explanation
Indices: 1876--1927 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
1866 TAGTAGGGGT
* *
1876 GAACGAATAAATTTTAGAGAGGAGC
1 GAACGAATAAACTTCAGAG-GGAGC
**
1901 GAACTCATAAACTTCAGAGGGAGC
1 GAACGAATAAACTTCAGAGGGAGC
1925 GAA
1 GAA
1928 AACAGATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.42, C:0.13, G:0.27, T:0.17
Consensus pattern (24 bp):
GAACGAATAAACTTCAGAGGGAGC
Found at i:3293 original size:9 final size:9
Alignment explanation
Indices: 3281--3314 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3271 TAATATTTTG
3281 TATTTAATT
1 TATTTAATT
*
3290 TATTTAA-G
1 TATTTAATT
3298 TATTTAATT
1 TATTTAATT
3307 TATTTAAT
1 TATTTAAT
3315 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:3320 original size:17 final size:17
Alignment explanation
Indices: 3280--3318 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3270 TTAATATTTT
3280 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
3297 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
3314 -TATTT
1 GTATTT
3319 TACTTAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:3823 original size:12 final size:12
Alignment explanation
Indices: 3806--3831 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3796 ATAAAGTTGA
3806 TAAGTTGAATTT
1 TAAGTTGAATTT
3818 TAAGTTGAATTT
1 TAAGTTGAATTT
3830 TA
1 TA
3832 CTTGTCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TAAGTTGAATTT
Found at i:4112 original size:21 final size:21
Alignment explanation
Indices: 4070--4112 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4060 TTTCTGGGCT
* *
4070 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
4091 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
4112 A
1 A
4113 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:5714 original size:103 final size:103
Alignment explanation
Indices: 5489--5706 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
5479 GTCGAGGGTC
5489 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
* *
5554 TTGATCCTTGGCATATATATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
* *
5592 TATGTGGTCCTTCGGGACATATATGTATTCTTTTGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
* *
5657 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
5695 TATGTGGTCCTT
1 TATGTGGTCCTT
5707 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
Found at i:5756 original size:23 final size:23
Alignment explanation
Indices: 5723--5790 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
5713 ATTATTATAT
*
5723 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGTAATTCTACGC
* *
5746 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGTAATTCTACGC
* *
5769 GGCACTTCGGTGTAATTATACG
1 GGCACTACGGTGTAATTCTACG
5791 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGTAATTCTACGC
Found at i:9365 original size:21 final size:21
Alignment explanation
Indices: 9323--9365 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9313 TTTATGGGCT
* *
9323 AGGGGAATTGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
9344 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
9365 A
1 A
9366 ACAAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:10951 original size:103 final size:103
Alignment explanation
Indices: 10726--10943 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
10716 GTCGAGGGTC
*
10726 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAATTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
10791 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
10829 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
10894 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
10932 TATGTGGTCCTT
1 TATGTGGTCCTT
10944 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:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:10997 original size:23 final size:23
Alignment explanation
Indices: 10960--11027 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
10950 ATTATTATAT
*
10960 GGCACTACGGTGCAATTCTACGC
1 GGCACTCCGGTGCAATTCTACGC
* *
10983 GGTACTCCGGTGCAATTCTACGT
1 GGCACTCCGGTGCAATTCTACGC
* *
11006 GGCACTTCGGTGCAATTATACG
1 GGCACTCCGGTGCAATTCTACG
11028 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTCTACGC
Found at i:14074 original size:25 final size:25
Alignment explanation
Indices: 14057--14119 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
14047 TGTATTTAGT
14057 ACTTTTTATTGTAGTTGTTTATTGG
1 ACTTTTTATTGTAGTTGTTTATTGG
14082 ACTTTTTATTGTAGTTGTTTATTGG
1 ACTTTTTATTGTAGTTGTTTATTGG
14107 ACTTTTTATTGTA
1 ACTTTTTATTGTA
14120 ATTTTTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.17, C:0.05, G:0.17, T:0.60
Consensus pattern (25 bp):
ACTTTTTATTGTAGTTGTTTATTGG
Found at i:14124 original size:12 final size:12
Alignment explanation
Indices: 14055--14125 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
14045 TTTGTATTTA
14055 GTACTTTTTATT
1 GTACTTTTTATT
*
14067 GTAGTTGTTTATT
1 GTACTT-TTTATT
*
14080 GGACTTTTTATT
1 GTACTTTTTATT
*
14092 GTAGTTGTTTATT
1 GTACTT-TTTATT
*
14105 GGACTTTTTATT
1 GTACTTTTTATT
*
14117 GTAATTTTT
1 GTACTTTTT
14126 TTATTTATCA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
12 28 0.58
13 20 0.42
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.62
Consensus pattern (12 bp):
GTACTTTTTATT
Found at i:17601 original size:16 final size:18
Alignment explanation
Indices: 17580--17625 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
17570 ATATTTTTTC
17580 AAATAATCATAAT-AA-A
1 AAATAATCATAATAAATA
17596 AAATAAGT-ATAATAAATA
1 AAATAA-TCATAATAAATA
*
17614 AAATTATCATAA
1 AAATAATCATAA
17626 AATTACCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 11 0.44
17 4 0.16
18 10 0.40
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (18 bp):
AAATAATCATAATAAATA
Found at i:18760 original size:6 final size:6
Alignment explanation
Indices: 18751--18827 Score: 73
Period size: 6 Copynumber: 12.8 Consensus size: 6
18741 GGGAGGGGGC
* * * * * *
18751 GGTGGA GGTGGA GGTGGT GGAGGA GGAGGA GGAGGT GGTGGA GGCGGA
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA GGTGGA
* * *
18799 GGGGGA GGTGGA GGTGGC GGCGGA GGTGG
1 GGTGGA GGTGGA GGTGGA GGTGGA GGTGG
18828 GAGTGGGGGT
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.16, C:0.04, G:0.69, T:0.12
Consensus pattern (6 bp):
GGTGGA
Found at i:18817 original size:21 final size:21
Alignment explanation
Indices: 18754--18824 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
18744 AGGGGGCGGT
* *
18754 GGAGGTGGAGGTGGTGGAGGA
1 GGAGGAGGAGGTGGTGGAGGC
18775 GGAGGAGGAGGTGGTGGAGGC
1 GGAGGAGGAGGTGGTGGAGGC
* * *
18796 GGAGGGGGAGGTGGAGGTGGC
1 GGAGGAGGAGGTGGTGGAGGC
*
18817 GGCGGAGG
1 GGAGGAGG
18825 TGGGAGTGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.17, C:0.04, G:0.69, T:0.10
Consensus pattern (21 bp):
GGAGGAGGAGGTGGTGGAGGC
Found at i:24576 original size:15 final size:15
Alignment explanation
Indices: 24555--24614 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
24545 CCGGATGTTA
24555 CGGGTACCCGATAAT
1 CGGGTACCCGATAAT
* **
24570 AGGGTACCCGGATTTT
1 CGGGTACCC-GATAAT
*
24586 GCGGGTACCCGGTAAT
1 -CGGGTACCCGATAAT
24602 CGGGTACCCGATA
1 CGGGTACCCGATA
24615 CCTGGTTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
15 20 0.57
16 7 0.20
17 8 0.23
ACGTcount: A:0.22, C:0.25, G:0.32, T:0.22
Consensus pattern (15 bp):
CGGGTACCCGATAAT
Found at i:24579 original size:32 final size:32
Alignment explanation
Indices: 24543--24611 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
24533 CCGTGTCCCG
24543 ACCCGGATGTTACGGGTACCCGATAATAGGGT
1 ACCCGGATGTTACGGGTACCCGATAATAGGGT
* * * *
24575 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGATAATAGGGT
24607 ACCCG
1 ACCCG
24612 ATACCTGGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.20, C:0.26, G:0.32, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGATAATAGGGT
Found at i:25072 original size:3 final size:3
Alignment explanation
Indices: 25055--25122 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
25045 TTTTTCCATT
* * * *
25055 TTA TT- TTA ATA TTA TTA TTA ATA CTA TTA TT- TTA TTA ATA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * *
25102 TAA TAA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
25123 AATAATAATA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:25091 original size:17 final size:18
Alignment explanation
Indices: 25064--25122 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
25054 TTTATTTTAA
25064 TATTATTATTAATACTAT
1 TATTATTATTAATACTAT
*
25082 TATT-TTATTAATATTAT
1 TATTATTATTAATACTAT
* * *
25099 TA--ATAATAAATATTAT
1 TATTATTATTAATACTAT
25115 TATTATTA
1 TATTATTA
25123 AATAATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 13 0.38
17 14 0.41
18 7 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATTATTAATACTAT
Found at i:25867 original size:39 final size:36
Alignment explanation
Indices: 25812--25939 Score: 107
Period size: 36 Copynumber: 3.5 Consensus size: 36
25802 TATATCTATA
*
25812 TATATATTATATAGTTTGCAAACGGTTTTTGAAAATATG
1 TATATAATATATAGTTT-CAAACGGTTTTTG-AAA-ATG
* * ***
25851 TATATAATATAAAGTTTCTAATTTTTTTTGAAAATG
1 TATATAATATATAGTTTCAAACGGTTTTTGAAAATG
* ** *
25887 TATATAATATATAGTTTTTAAAAC-ACTTTTGAAAA-C
1 TATATAATATATAG--TTTCAAACGGTTTTTGAAAATG
25923 TATATAATATATAGTTT
1 TATATAATATATAGTTT
25940 TTAAAATCAT
Statistics
Matches: 74, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
34 3 0.04
36 30 0.41
37 12 0.16
38 14 0.19
39 15 0.20
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (36 bp):
TATATAATATATAGTTTCAAACGGTTTTTGAAAATG
Found at i:25975 original size:37 final size:37
Alignment explanation
Indices: 25875--26076 Score: 279
Period size: 37 Copynumber: 5.5 Consensus size: 37
25865 TTTCTAATTT
25875 TTTTTGAAAA-TGTATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAACT-TATATAATATATAGTTTTTAAAACA
*
25912 CTTTTGAAAAC-TATATAATATATAGTTTTTAAAATCA
1 TTTTTGAAAACTTATATAATATATAGTTTTTAAAA-CA
*
25949 -TTTTGAAAACTTATATAATATTTAGTTTTTGAAAACA
1 TTTTTGAAAACTTATATAATATATAGTTTTT-AAAACA
* *
25986 TTTTTGAAAACTTATA-AAAATATAGTTTTGAAAACA
1 TTTTTGAAAACTTATATAATATATAGTTTTTAAAACA
* *
26022 TTTTTGGAAACTTATATAATATATAATTTTTGAAAACA
1 TTTTTGAAAACTTATATAATATATAGTTTTT-AAAACA
26060 TTTTTGAAAA-TTATATA
1 TTTTTGAAAACTTATATA
26077 GTTTTTAAAA
Statistics
Matches: 148, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
36 54 0.36
37 60 0.41
38 34 0.23
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (37 bp):
TTTTTGAAAACTTATATAATATATAGTTTTTAAAACA
Found at i:26138 original size:33 final size:30
Alignment explanation
Indices: 26041--26140 Score: 128
Period size: 31 Copynumber: 3.2 Consensus size: 30
26031 ACTTATATAA
* *
26041 TATATAATTTTTGAAAACATTTTTGAAAAT
1 TATATAGTTTTTAAAAACATTTTTGAAAAT
26071 TATATAGTTTTTAAAAACATTTTTTGAAAAT
1 TATATAGTTTTTAAAAACA-TTTTTGAAAAT
* *
26102 TATATAGTTTTTTAAAAAACACTTTTGAAATTT
1 TATATAG-TTTTT-AAAAACATTTTTGAAA-AT
26135 TATATA
1 TATATA
26141 TAATATATAG
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
30 17 0.27
31 18 0.29
32 13 0.21
33 14 0.23
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (30 bp):
TATATAGTTTTTAAAAACATTTTTGAAAAT
Found at i:26219 original size:6 final size:6
Alignment explanation
Indices: 26208--26237 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
26198 AATTACACTT
26208 TTTATA TTTATA TTTATA TTTATTA TTTAT
1 TTTATA TTTATA TTTATA TTTA-TA TTTAT
26238 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATA
Found at i:26236 original size:13 final size:13
Alignment explanation
Indices: 26208--26247 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
26198 AATTACACTT
26208 TTTATATTTA-TA
1 TTTATATTTATTA
26220 TTTATATTTATTA
1 TTTATATTTATTA
26233 TTTAT-TATTATTA
1 TTTATAT-TTATTA
26246 TT
1 TT
26248 ATTATTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTATATTTATTA
Found at i:26240 original size:3 final size:3
Alignment explanation
Indices: 26227--26256 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
26217 ATATTTATAT
26227 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
26257 TTTGTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:26243 original size:19 final size:18
Alignment explanation
Indices: 26207--26253 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
26197 AAATTACACT
26207 TTTTA-TATTTATATTTA
1 TTTTATTATTTATATTTA
26224 TATTTATTATTTAT-TATTA
1 T-TTTATTATTTATAT-TTA
26243 TTATTATTATT
1 TT-TTATTATT
26254 ATTTTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.04
18 6 0.23
19 19 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATTATTTATATTTA
Found at i:30551 original size:100 final size:98
Alignment explanation
Indices: 30378--30637 Score: 380
Period size: 100 Copynumber: 2.6 Consensus size: 98
30368 ATATTACATA
*
30378 TATACAATAAAGCTTGAGCTGTCCCTCTAAAGCAATTGGTTAAACACCCCGACTTTATGGATAAG
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACACCCCG-CTTTATGGATAAG
30443 ATTCAGCTAAGCCTGATAAAGGTAATTATAATATC
65 ATTCAGCT-AGCCTGATAAAGGTAATTATAATATC
* * * * * *
30478 TATACGATAAAGCTTGAGTTGTCCCTCTAGAGCTATTGGTTAAACGCCCCAGCTGTATGGATAAT
1 TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACACCCC-GCTTTATGGATAAG
*
30543 ATTCAGCTAGCCTGATAAAGGTGATTATAATATC
65 ATTCAGCTAGCCTGATAAAGGTAATTATAATATC
*
30577 TATACAATGATA--TTGAGCTGTCCCTCTAGAGCAATTGGTTAAACACCCCGGCTTTATGGAT
1 TATACAAT-AAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACACCCC-GCTTTATGGAT
30638 CCAACTAGCC
Statistics
Matches: 143, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
98 44 0.31
99 32 0.22
100 66 0.46
101 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (98 bp):
TATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACACCCCGCTTTATGGATAAGA
TTCAGCTAGCCTGATAAAGGTAATTATAATATC
Found at i:33337 original size:84 final size:84
Alignment explanation
Indices: 31763--33325 Score: 1805
Period size: 84 Copynumber: 18.7 Consensus size: 84
31753 GAAACTATTG
* * * *
31763 GCAGCATAACTCAAGGCAAGAAGGGTTATCTACCAACAAAAGACCTTCGAGTTTGATTACACTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
31828 GCTCAAAGGCACAACATTT
66 GCTCCAAGGCACATCATTT
* * * * *
31847 GTAGCATAGA-TCAAGGCGAGAAGGGCTAACTGCCAACAAAAGACCTTCGAGTTCGACTACACTC
1 GCAGCATA-ACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC
* * *
31911 ATCTCCAAGGAACTTCATTT
65 AGCTCCAAGGCACATCATTT
* * * * *
31931 GCAGCATAACTCAAGGCTAGAAGAGTTATCTGCCAACAAAAGACATCCGAGTTCAACTACGCTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
31996 TCTCCAAGGCACTTCATTT
66 GCTCCAAGGCACATCATTT
* *
32015 GCAGCATAACTCAAGGCTAGAAGAGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
32080 GCTCCAAGGCACATTATTT
66 GCTCCAAGGCACATCATTT
** * * ** * ** * *
32099 GCAAAATAGCTCAAGGAAAGAAGGACTATATATCGACAAAAGACCTT--AGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
32162 GCTCTAAGGCACATCATTT
66 GCTCCAAGGCACATCATTT
* * * * *
32181 GTAGCATAACTCAAGGCTAGAAGGGTTATCTACCAACAAAATACCCTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
32246 GCTCCAAGGCACATCATTT
66 GCTCCAAGGCACATCATTT
* * * * * * *
32265 GCAACATAGCTCAAGGCAAGAAAGGTTATTTTCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
32330 GCTCAAAGGCACAACATTT
66 GCTCCAAGGCACATCATTT
* * * * *
32349 GCATCATAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
32414 GCTCCAAGGCACATCATTT
66 GCTCCAAGGCACATCATTT
* * * * * **
32433 ACAGCATAACTCAAGGCAATG-AGGGTTATCTACCAACACAAGACCTTCGAGTTCAATTATACTC
1 GCAGCATAACTCAAGGCAA-GAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC
* * *
32497 GGCTCAAATGCACATCATTT
65 AGCTCCAAGGCACATCATTT
* * * *
32517 GCAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAATAAAAGACCTTTGAGTTCGATTACGCTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
32582 ACTCTAAGGCACATCATTT
66 GCTCCAAGGCACATCATTT
* * * * *
32601 GTAACATAACTCAAGGAAAGAAGGGTTATTTGCCAACAAAAGACCTTCGAGTTCGACTATGCTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
32666 GCTCCAAGGCACATCATTT
66 GCTCCAAGGCACATCATTT
* * * * * * *
32685 GTAGTATAGCTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACACTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
32750 ACTCCAAGGCACATCATTT
66 GCTCCAAGGCACATCATTT
* * * *
32769 GCAGCATAGCTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACGCTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
32834 GCTTCAAGGCACATCATTT
66 GCTCCAAGGCACATCATTT
* * *
32853 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAAGACCTTCGAGTTTGACTACGCTC
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAA-CAAAAGACCTTCGAGTTCGACTACGCTC
**
32918 AGCTCCAAGGCGTATCATTT
65 AGCTCCAAGGCACATCATTT
* * * *
32938 GCAGCATAGCTCAAGGCTAA-AAGAGTTATCTGCCACCAAAAGACCATCGAGTTCGACTACGCTC
1 GCAGCATAACTCAAGGC-AAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC
*
33002 AGCTCCAAGGCATATCATTT
65 AGCTCCAAGGCACATCATTT
* * * * * * * *
33022 GTAGCATAACTCAAGGCTAGAAGGATTATCTGCCGATAAAAAACCTTTGAGTTCGACTACGCTTA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
*
33087 GCTCTAAGGCACATCATTT
66 GCTCCAAGGCACATCATTT
** * * * * * * *
33106 ATAGTATAGCTTAAGTCGAGAAGGGTTATATG-C--CAAAA-ACCGTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
* *
33167 GCTCCATGGCACATTATTT
66 GCTCCAAGGCACATCATTT
* * * * * * * *
33186 GCAGCATAA-TGCAAGGCTATAAAGGTTATTTGCCGACAAAAAACCTTTGAGTTCGACTATGCTC
1 GCAGCATAACT-CAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC
**
33250 AGCTTAAAGGCACATCATTT
65 AGCTCCAAGGCACATCATTT
* * * * *
33270 GCAGCATAGCTCAAGGCAATAAGGGCTATCTGCCACCAAAAGGCCTTCGAGTTCGA
1 GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGA
33326 TAGCATTCAG
Statistics
Matches: 1265, Mismatches: 199, Indels: 30
0.85 0.13 0.02
Matches are distributed among these distances:
79 1 0.00
80 56 0.04
81 5 0.00
82 66 0.05
83 9 0.01
84 1051 0.83
85 76 0.06
86 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (84 bp):
GCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCA
GCTCCAAGGCACATCATTT
Found at i:34125 original size:37 final size:35
Alignment explanation
Indices: 34003--34191 Score: 245
Period size: 37 Copynumber: 5.2 Consensus size: 35
33993 TGAAAATACG
*
34003 TATATAATATATAGTTTCTAAAAACATTTTG-AAAT
1 TATATAATATATAGTTT-TTAAAACATTTTGAAAAT
* * *
34038 GTGTATAATATATAGTTTTCAAAACACTTTTGAAAAC
1 -TATATAATATATAGTTTTTAAAACA-TTTTGAAAAT
34075 TATATAATATATAGTTTTTAAAACATTTTAGAAAAT
1 TATATAATATATAGTTTTTAAAACATTTT-GAAAAT
34111 ATATATAATATATAGTTTTTAAAATCATTTTGAAAACT
1 -TATATAATATATAGTTTTTAAAA-CATTTTGAAAA-T
*
34149 TATATAATATATAGTTTTTGAAAATATTTTTGAAAAT
1 TATATAATATATAGTTTTT-AAAACA-TTTTGAAAAT
34186 TATATA
1 TATATA
34192 GTTTTTAAAA
Statistics
Matches: 138, Mismatches: 7, Indels: 15
0.86 0.04 0.09
Matches are distributed among these distances:
35 11 0.08
36 49 0.36
37 58 0.42
38 20 0.14
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAAT
Found at i:34234 original size:32 final size:30
Alignment explanation
Indices: 34156--34255 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 30
34146 ACTTATATAA
* *
34156 TATATAGTTTTTGAAAATATTTTTGAAAAT
1 TATATAGTTTTTAAAAACATTTTTGAAAAT
34186 TATATAGTTTTTAAAAACATTTTTTGAAAAT
1 TATATAGTTTTTAAAAACA-TTTTTGAAAAT
*
34217 TATATAGTTTTTTAAAAAACACTTTTGAAAATT
1 TATATAG-TTTTT-AAAAACATTTTTGAAAA-T
34250 TATATA
1 TATATA
34256 TAATATATAG
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
30 17 0.27
31 18 0.29
32 14 0.22
33 14 0.22
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (30 bp):
TATATAGTTTTTAAAAACATTTTTGAAAAT
Found at i:34253 original size:33 final size:31
Alignment explanation
Indices: 34156--34255 Score: 132
Period size: 30 Copynumber: 3.2 Consensus size: 31
34146 ACTTATATAA
* *
34156 TATATAGTTTTTGAAAATAT-TTTTGAAAAT
1 TATATAGTTTTTAAAAACATCTTTTGAAAAT
*
34186 TATATAGTTTTTAAAAACATTTTTTGAAAAT
1 TATATAGTTTTTAAAAACATCTTTTGAAAAT
34217 TATATAGTTTTTTAAAAAACA-CTTTTGAAAATT
1 TATATAG-TTTTT-AAAAACATCTTTTGAAAA-T
34250 TATATA
1 TATATA
34256 TAATATATAG
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
30 18 0.29
31 17 0.27
32 14 0.22
33 14 0.22
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (31 bp):
TATATAGTTTTTAAAAACATCTTTTGAAAAT
Found at i:34275 original size:42 final size:38
Alignment explanation
Indices: 34217--34323 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 38
34207 TTTTGAAAAT
34217 TATATAGTTTTTTAAAAAACACTTTTGAAAATTTATATATAA
1 TATATAGTTTTTTAAAAAA-ACTTTTGAAAA---ATATATAA
* * *
34259 TATATAGTTTTTTAAAAAAACATTTTTAAAAATGTATAT
1 TATATAGTTTTTTAAAAAAAC-TTTTGAAAAATATATAA
*
34298 TATATAGTTTTTTTAAAAATACTTTT
1 TATATAG-TTTTTTAAAAAAACTTTT
34324 TATATTTATA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
39 17 0.29
40 13 0.22
41 2 0.03
42 27 0.46
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.49
Consensus pattern (38 bp):
TATATAGTTTTTTAAAAAAACTTTTGAAAAATATATAA
Found at i:34333 original size:6 final size:6
Alignment explanation
Indices: 34322--34350 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
34312 AAAAATACTT
34322 TTTATA TTTATA TTTATA TTTATA TTTAT
1 TTTATA TTTATA TTTATA TTTATA TTTAT
34351 TATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:34361 original size:18 final size:18
Alignment explanation
Indices: 34320--34361 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
34310 TTAAAAATAC
34320 TTTTTATATTTATATTTA
1 TTTTTATATTTATATTTA
*
34338 TATTTATATTTAT-TATTA
1 TTTTTATATTTATAT-TTA
34356 TTTTTA
1 TTTTTA
34362 GGTCCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATATTTATATTTA
Found at i:34893 original size:22 final size:22
Alignment explanation
Indices: 34865--34919 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
34855 GGCTATATTA
*
34865 GTCCTTC-AGGACGTATCCAGTG
1 GTCCTTCGA-GACGTATCCAGAG
34887 GTCCTTCGAGACGTATCCAGAG
1 GTCCTTCGAGACGTATCCAGAG
34909 GTCCTTCGAGA
1 GTCCTTCGAGA
34920 AATAGTGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.25
Consensus pattern (22 bp):
GTCCTTCGAGACGTATCCAGAG
Found at i:34953 original size:18 final size:18
Alignment explanation
Indices: 34908--34957 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
34898 CGTATCCAGA
* *
34908 GGTCCTTCGAGAAATAGT
1 GGTCCTTCGGGACATAGT
34926 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
34944 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
34958 AATACTGAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.26
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:39776 original size:22 final size:22
Alignment explanation
Indices: 39750--39871 Score: 190
Period size: 22 Copynumber: 5.5 Consensus size: 22
39740 GGGTATATTA
*
39750 GTCCTTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
*
39772 ATCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
39794 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* * **
39816 GTCCTTTGGAACGTATCTTGTG
1 GTCCTTCGGGACGTATCCAGTG
39838 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
39860 GTCCTTCGGGAC
1 GTCCTTCGGGAC
39872 ATAGTGGTTA
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 89 1.00
ACGTcount: A:0.14, C:0.25, G:0.30, T:0.30
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:41292 original size:21 final size:20
Alignment explanation
Indices: 41268--41343 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 20
41258 AAATGCCTGA
* *
41268 GGGTATCGGTACCTAAGTAAG
1 GGGTATCGATACCTAA-TAGG
41289 GGGTATCGATACC-ATATCATGG
1 GGGTATCGATACCTA-AT-A-GG
*
41311 GGGTATCGATACCTACTAGG
1 GGGTATCGATACCTAATAGG
*
41331 GGGTATCGGTACC
1 GGGTATCGATACC
41344 ATCCGAGCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 16 0.34
21 15 0.32
22 15 0.32
23 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCTAATAGG
Found at i:41316 original size:22 final size:21
Alignment explanation
Indices: 41288--41345 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
41278 ACCTAAGTAA
41288 GGGGTATCGATACCATA-TCATG
1 GGGGTATCGATACCATACT-A-G
41310 GGGGTATCGATACC-TACTAG
1 GGGGTATCGATACCATACTAG
*
41330 GGGGTATCGGTACCAT
1 GGGGTATCGATACCAT
41346 CCGAGCATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 14 0.42
21 4 0.12
22 15 0.45
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (21 bp):
GGGGTATCGATACCATACTAG
Found at i:41334 original size:20 final size:19
Alignment explanation
Indices: 41268--41343 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 19
41258 AAATGCCTGA
* *
41268 GGGTATCGGTACCTAAGTAAG
1 GGGTATCGATACCT-A-TAGG
41289 GGGTATCGATACCATATCATGG
1 GGGTATCGATACC-TAT-A-GG
41311 GGGTATCGATACCTACTAGG
1 GGGTATCGATACCTA-TAGG
*
41331 GGGTATCGGTACC
1 GGGTATCGATACC
41344 ATCCGAGCAT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 15 0.31
21 17 0.35
22 16 0.33
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (19 bp):
GGGTATCGATACCTATAGG
Found at i:41433 original size:75 final size:75
Alignment explanation
Indices: 41305--41496 Score: 314
Period size: 75 Copynumber: 2.5 Consensus size: 75
41295 CGATACCATA
* *
41305 TCATGGGGGTATCGATA-CCTACTAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCGG
1 TCATAGGGGTATCGGTACCCTA-TAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCGG
41369 AACCAAAATGT
65 AACCAAAATGT
41380 TCATAGGGGTATCGGTACCCTATAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCGGA
1 TCATAGGGGTATCGGTACCCTATAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCGGA
41445 ACCAAAATGT
66 ACCAAAATGT
* * *
41455 TCATAGGGGTATCGGTACCATATATGAGGGTATCGATACCAT
1 TCATAGGGGTATCGGTACCCTATA-GGGGGTATCGGTACCAT
41497 ACTAAATAAA
Statistics
Matches: 110, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
75 91 0.83
76 19 0.17
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (75 bp):
TCATAGGGGTATCGGTACCCTATAGGGGGTATCGGTACCATCCGAGCATTCTGTTATTTCTCGGA
ACCAAAATGT
Found at i:41734 original size:29 final size:29
Alignment explanation
Indices: 41713--41770 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
41703 AAACTTTGAA
41713 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
41742 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
41771 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:41760 original size:30 final size:30
Alignment explanation
Indices: 41713--41772 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
41703 AAACTTTGAA
41713 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
41742 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
41773 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:42284 original size:2 final size:2
Alignment explanation
Indices: 42277--42302 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42267 GATCATATGA
42277 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
42303 GAAAGGATAA
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:46073 original size:17 final size:16
Alignment explanation
Indices: 46042--46075 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
46032 CACGTGAGGA
46042 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
46058 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
46075 T
1 T
46076 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:55207 original size:17 final size:16
Alignment explanation
Indices: 55176--55209 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
55166 CACGTGAGGA
55176 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
55192 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
55209 T
1 T
55210 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:58943 original size:12 final size:10
Alignment explanation
Indices: 58901--58962 Score: 65
Period size: 10 Copynumber: 6.1 Consensus size: 10
58891 CTCATTCATC
58901 AGAAAAAAGA
1 AGAAAAAAGA
58911 AGAAAAAAGA
1 AGAAAAAAGA
*
58921 AAAAAAAAGA
1 AGAAAAAAGA
*
58931 TGAAAAAAG-
1 AGAAAAAAGA
58940 AGATGAAAAAGA
1 AGA--AAAAAGA
58952 A-AAGAAAAGA
1 AGAA-AAAAGA
58962 A
1 A
58963 ATTGAATCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
9 3 0.07
10 33 0.75
11 7 0.16
12 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (10 bp):
AGAAAAAAGA
Found at i:58960 original size:31 final size:30
Alignment explanation
Indices: 58902--58961 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
58892 TCATTCATCA
58902 GAAAAAAGAAGAAAAAAGAAAAAAAAAGAT
1 GAAAAAAGAAGAAAAAAGAAAAAAAAAGAT
*
58932 GAAAAAAG-AGATGAAAAAGAAAAGAAAAGA
1 GAAAAAAGAAGA--AAAAAGAAAAAAAAAGA
58962 AATTGAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 3 0.11
30 8 0.30
31 16 0.59
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (30 bp):
GAAAAAAGAAGAAAAAAGAAAAAAAAAGAT
Found at i:62102 original size:265 final size:265
Alignment explanation
Indices: 61712--62547 Score: 1188
Period size: 265 Copynumber: 3.2 Consensus size: 265
61702 AGTCCTTAAG
* ** * *
61712 GCCATCTGTAATTCTTTTGAGCATGATGTTTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGC
1 GCCATCTGTAAGTCTTTCAAGCATGATG-CTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGC
* * *
61777 AAGATAAT-AAGTCCTTCAGG-CTATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATA
65 AAGATGATAAAG-CCTTCGGGTC-ATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATT
* *
61840 TTAAAAACTAAGCCTAATTTTAAGGGGTTTTCTAATTATCTTAAAAGAGTTGTTAAATGAAGCTA
128 TTAAAAACTAAGCCTAATTTTAAGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAATGAAGCTA
* * *
61905 AGCCTAATAAAGGGGTTCATTGACAAATAAGAAAGTAAGCTTTCGAGGGTTTCTTGATTCGTAAG
193 AGCCTAACAAAGGGGTTCATTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTCGTAAG
61970 TCCTTTGA
258 TCCTTTGA
* **
61978 GCCATCTGTAAGTCTTTCAAGCATGATGTTTAAATATTTCGGGTCATCTGTAAGCCTTTCGAGCA
1 GCCATCTGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCA
*
62043 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCTA-GATGCTTTCAAATGAGATTTT
66 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGC-AGGATGTTTTCAAATGAGATTTT
* * *
62107 AAAAACTAAACC----TTTCAGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAG
130 AAAAACTAAGCCTAATTTTAAGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAATGAAGCTAAG
* * *
62168 CCTAACAAAGGGGTTCCTTGACAACTATA-AAACTAAGCTTTTGAAGGTTTCTTGATTCGTAAGT
195 CCTAACAAAGGGGTTCATTGACAACTA-AGAAACTAAGCTTTCGAGGGTTTCTTGATTCGTAAGT
* *
62232 CCTTCGG
259 CCTTTGA
* *
62239 GTCACCTGTAAGTCTTT-AGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGC
1 GCCATCTGTAAGTCTTTCA-AGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGC
* *
62303 AAGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAATGCAGGATATTTTCAAATGAGATTTT
65 AAGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTT
* *
62368 AGAAACTAAGCCTAATTTTAAGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAATGAAGCTAAA
130 AAAAACTAAGCCTAATTTTAAGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAATGAAGCTAAG
* * * *
62433 CCTAACAAAAGGGTTCTTTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTAATTTGTAAGTC
195 CCTAACAAAGGGGTTCATTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTCGTAAGTC
*
62498 C-TTCA
260 CTTTGA
* * *
62503 GGCCATCTATATGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
1 -GCCATCTGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGT
62548 TATCCATAAG
Statistics
Matches: 507, Mismatches: 50, Indels: 27
0.87 0.09 0.05
Matches are distributed among these distances:
260 2 0.00
261 233 0.46
262 1 0.00
264 2 0.00
265 239 0.47
266 30 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (265 bp):
GCCATCTGTAAGTCTTTCAAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTCGAGCA
AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTA
AAAACTAAGCCTAATTTTAAGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAATGAAGCTAAGC
CTAACAAAGGGGTTCATTGACAACTAAGAAACTAAGCTTTCGAGGGTTTCTTGATTCGTAAGTCC
TTTGA
Found at i:62326 original size:41 final size:42
Alignment explanation
Indices: 62232--62327 Score: 131
Period size: 42 Copynumber: 2.3 Consensus size: 42
62222 ATTCGTAAGT
* * * * *
62232 CCTTCGGGTCACCTGTAAGTCTTTAGAGCATGATGCTTAAAT
1 CCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGCATAAAG
*
62274 CCTTCGGGTCATCTGTAAGCCTTTCGAGCAAGATG-ATAAAG
1 CCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGCATAAAG
62315 CCTTCGGGTCATC
1 CCTTCGGGTCATC
62328 CATAAGACCT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 17 0.35
42 31 0.65
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (42 bp):
CCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGCATAAAG
Found at i:63115 original size:3 final size:3
Alignment explanation
Indices: 63093--63141 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
63083 TTTTCCCATT
*
63093 TTA TT- TTA ATA TTA TT- 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
63139 TTA
1 TTA
63142 AATAATAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:63195 original size:24 final size:21
Alignment explanation
Indices: 63168--63218 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 21
63158 AATATATTAC
63168 AGGCCCAATTTACAAGGGACCCGA
1 AGGCCCAATTTACAA---ACCCGA
63192 AGGCCC-ATTTACAAACCCGA
1 AGGCCCAATTTACAAACCCGA
63212 AGGCCCA
1 AGGCCCA
63219 GATCCAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 12 0.46
23 8 0.31
24 6 0.23
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.12
Consensus pattern (21 bp):
AGGCCCAATTTACAAACCCGA
Found at i:64465 original size:13 final size:14
Alignment explanation
Indices: 64421--64473 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 14
64411 TTAGTTTCAA
*
64421 TATTTTTAATTTAT
1 TATTTTTATTTTAT
* *
64435 TA-CTTTA-ATTAT
1 TATTTTTATTTTAT
64447 TATTTTTATTTTAT
1 TATTTTTATTTTAT
64461 T-TTTTTATTTTAT
1 TATTTTTATTTTAT
64474 ACTCATCACA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 6 0.18
13 20 0.61
14 7 0.21
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTTTATTTTAT
Found at i:64701 original size:2 final size:2
Alignment explanation
Indices: 64696--64724 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64686 TAATATATGA
64696 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
64725 AAGGATAATA
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
Done.