Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007579.1 Hibiscus syriacus cultivar Beakdansim tig00021617_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: 68603
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Found at i:3004 original size:21 final size:21
Alignment explanation
Indices: 2980--3024 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2970 TTTATAAACT
*
2980 ATAAAACAATATAATTTAAGA
1 ATAAAACAATATAATTTAAAA
** *
3001 ATAAATTAATTTAATTTAAAA
1 ATAAAACAATATAATTTAAAA
3022 ATA
1 ATA
3025 TTTAAATAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
ATAAAACAATATAATTTAAAA
Found at i:3084 original size:21 final size:22
Alignment explanation
Indices: 2987--3084 Score: 66
Period size: 21 Copynumber: 4.5 Consensus size: 22
2977 ACTATAAAAC
*
2987 AATATAATTTAAGAATA-AATT
1 AATATAATTTAAGAATATATTT
*
3008 AATTTAATTTAA-AA-ATATTT
1 AATATAATTTAAGAATATATTT
3028 AA-ATAATATT-AGAATA-ATTT
1 AATATAAT-TTAAGAATATATTT
* *
3048 AAATTATTTATGTTAAGAACATA-TT
1 -AA-TA-TAAT-TTAAGAATATATTT
3073 AATATAATTTAA
1 AATATAATTTAA
3085 ATCTATAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
19 6 0.10
20 15 0.25
21 18 0.30
22 3 0.05
23 3 0.05
24 7 0.12
25 7 0.12
26 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (22 bp):
AATATAATTTAAGAATATATTT
Found at i:3093 original size:13 final size:13
Alignment explanation
Indices: 3075--3099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3065 AACATATTAA
3075 TATAATTTAAATC
1 TATAATTTAAATC
3088 TATAATTTAAAT
1 TATAATTTAAAT
3100 ATTAATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATTTAAATC
Found at i:3386 original size:19 final size:20
Alignment explanation
Indices: 3358--3401 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3348 TAATTTAAAA
*
3358 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
3377 TAAATAATATTATAATAATT
1 TAAATAATATAAAAATAATT
3397 TAAAT
1 TAAAT
3402 CAATTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:7738 original size:15 final size:17
Alignment explanation
Indices: 7714--7750 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
7704 TAATCTGATC
*
7714 CAAATGTAAAAA-AATT
1 CAAATATAAAAATAATT
7730 -AAATATAAAAATAATT
1 CAAATATAAAAATAATT
7746 CAAAT
1 CAAAT
7751 GCATCGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (17 bp):
CAAATATAAAAATAATT
Found at i:9887 original size:26 final size:26
Alignment explanation
Indices: 9858--9912 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
9848 CACAATTCAC
* *
9858 ATCATAATTCAAATCAAACAATGATA
1 ATCATAATCCAAATCAAACAATAATA
* *
9884 ATCATTATCCAAATCAAACATTAATA
1 ATCATAATCCAAATCAAACAATAATA
9910 ATC
1 ATC
9913 CGAGTTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.51, C:0.18, G:0.02, T:0.29
Consensus pattern (26 bp):
ATCATAATCCAAATCAAACAATAATA
Found at i:9977 original size:26 final size:26
Alignment explanation
Indices: 9947--9997 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
9937 TTAAGAATAA
9947 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
*
9973 ATTATCCAAATGAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
9998 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:10621 original size:21 final size:20
Alignment explanation
Indices: 10591--10632 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
10581 TAATTTAAAT
*
10591 TTAATTTAATTTAAGAATTTA
1 TTAATATAATTTAA-AATTTA
*
10612 TTAATATAATTTTAAATTTA
1 TTAATATAATTTAAAATTTA
10632 T
1 T
10633 AATTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTAATATAATTTAAAATTTA
Found at i:13205 original size:49 final size:49
Alignment explanation
Indices: 13133--13230 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
13123 CAAATACATA
13133 GACAAATGATCCACGTTGTTACCTGTATGAAATTCAAAACCAAGAGTAT
1 GACAAATGATCCACGTTGTTACCTGTATGAAATTCAAAACCAAGAGTAT
* *
13182 GACAACTGATCCACGTTGTTACCTGTATGAAATTCAAAACCAATAGTAT
1 GACAAATGATCCACGTTGTTACCTGTATGAAATTCAAAACCAAGAGTAT
13231 AAAGACTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (49 bp):
GACAAATGATCCACGTTGTTACCTGTATGAAATTCAAAACCAAGAGTAT
Found at i:24436 original size:3 final size:3
Alignment explanation
Indices: 24428--24479 Score: 70
Period size: 3 Copynumber: 17.0 Consensus size: 3
24418 GGCCTGCAAA
*
24428 AAT AAT AAT AAT AATT AAT AA- ACAT AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
24474 AAT AAT
1 AAT AAT
24480 TAAAATTAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 1 0.02
3 39 0.89
4 4 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:24880 original size:40 final size:42
Alignment explanation
Indices: 24783--25018 Score: 153
Period size: 40 Copynumber: 5.5 Consensus size: 42
24773 GTGATAACAT
* * ** *
24783 GGTTCCTACGTGATGAGTACGGT-TGGTTATCTATGGTTGACAC
1 GGTTCCTACGTGATGAGGACGATCTGG--ATCTGGGGATGACAC
*
24826 GGCTCCTACGTGATGAGGA-GATCTGG-TCTGGGGATGACAC
1 GGTTCCTACGTGATGAGGACGATCTGGATCTGGGGATGACAC
* * * *
24866 GATTCCTACATGATGAGGACGGT-TGGCCATCTTTAGGAAGGTGATAACAC
1 GGTTCCTACGTGATGAGGACGATCTGG--ATC--T--G--GG-GATGACAC
* ** *
24916 GGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTGACAC
1 GGTTCCTACGTGATGAGGACGATCTGG--ATCTGGGGATGACAC
*
24959 GGCTCCTACGTGATGAGGA-GATCTGG-TCTGGGGATGACAC
1 GGTTCCTACGTGATGAGGACGATCTGGATCTGGGGATGACAC
* *
24999 GATTCCTACATGATGAGGAC
1 GGTTCCTACGTGATGAGGAC
25019 AGTTGGCCAT
Statistics
Matches: 150, Mismatches: 28, Indels: 32
0.71 0.13 0.15
Matches are distributed among these distances:
40 57 0.38
41 2 0.01
42 3 0.02
43 50 0.33
44 1 0.01
45 1 0.01
47 1 0.01
48 1 0.01
49 2 0.01
50 32 0.21
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (42 bp):
GGTTCCTACGTGATGAGGACGATCTGGATCTGGGGATGACAC
Found at i:24894 original size:133 final size:133
Alignment explanation
Indices: 24687--25030 Score: 539
Period size: 133 Copynumber: 2.6 Consensus size: 133
24677 CGTCTAAGGG
* * * ** * * *
24687 TGACACAGTTCCTACGTGATGAGGAGATTTGGTC-GGTGGATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGG-GGATGACACGATTCCTACATGATGAGG
* * * *
24751 A-GTTCTGGCCATCTTTAGGAAGGTGATAACATGGTTCCTACGTGATGAGTACGGTTGGTTATCT
65 ACGGT-TGGCCATCTTTAGGAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
24815 ATGGT
129 ATGGT
24820 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGATTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGATTCCTACATGATGAGGA
24885 CGGTTGGCCATCTTTAGGAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
66 CGGTTGGCCATCTTTAGGAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
24950 GGT
131 GGT
24953 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGATTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGATTCCTACATGATGAGGA
*
25018 CAGTTGGCCATCT
66 CGGTTGGCCATCT
25031 AAAGGAGTTA
Statistics
Matches: 196, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
133 192 0.98
134 4 0.02
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.27
Consensus pattern (133 bp):
TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGATTCCTACATGATGAGGA
CGGTTGGCCATCTTTAGGAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAT
GGT
Found at i:25474 original size:30 final size:30
Alignment explanation
Indices: 25434--25492 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
25424 AAGATGATCT
*
25434 TGTTTTAAGAGAAAATGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAATGTTTCAAGAGAAAA
* *
25464 TGTTTCAAGAGAAAATGTTTTAAGTGAAA
1 TGTTTCAAGAGAAAATGTTTCAAGAGAAA
25493 CGACTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.32
Consensus pattern (30 bp):
TGTTTCAAGAGAAAATGTTTCAAGAGAAAA
Found at i:25492 original size:15 final size:15
Alignment explanation
Indices: 25434--25483 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
25424 AAGATGATCT
*
25434 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
25449 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
25464 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
25479 TGTTT
1 TGTTT
25484 TAAGTGAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:25720 original size:63 final size:64
Alignment explanation
Indices: 25649--25773 Score: 189
Period size: 64 Copynumber: 2.0 Consensus size: 64
25639 AAGGTTGGTA
* * *
25649 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* * *
25712 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
25774 GGATCTCATC
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 17 0.31
64 38 0.69
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:26065 original size:63 final size:65
Alignment explanation
Indices: 25961--26321 Score: 439
Period size: 67 Copynumber: 5.5 Consensus size: 65
25951 TTTCAAAATG
* ** *** * * *
25961 AACATATTCAAAGA-TTTACTTCAAAAGAAACGGTCTCAAGAGATACAAAATTCAT-TTT-AAGA
1 AACAAATTCAAAGATTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATT-TTGTTTCAA-A
26023 GA
64 GA
* *
26025 AACAGATTCAAAGA-TTT-TTTCAAAAGAAATTGTCTTAAGAGAGACAAAATTTTGTTTCCAAAG
1 AACAAATTCAAAGATTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT-CAAAG
26088 A
65 A
* *
26089 AACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAAA
1 AACAAATTCAAAGA-TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT-CAAA
26154 GA
64 GA
*
26156 AACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAA
1 AACAAATTCAAAGA-TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT-CAAA
26221 GA
64 GA
26223 AACAAACTT-AAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAA
1 AACAAA-TTCAAAGA-TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT-CAA
26287 AGA
63 AGA
26290 AACAAACTT-AAAGATTTTTGTTTCAAAAGAAA
1 AACAAA-TTCAAAGA-TTTTGTTTCAAAAGAAA
26322 CAATCTCAAA
Statistics
Matches: 277, Mismatches: 13, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
62 1 0.00
63 32 0.12
64 31 0.11
65 2 0.01
66 3 0.01
67 207 0.75
68 1 0.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (65 bp):
AACAAATTCAAAGATTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAGA
Found at i:26108 original size:30 final size:30
Alignment explanation
Indices: 26074--26338 Score: 143
Period size: 30 Copynumber: 8.1 Consensus size: 30
26064 AGAGACAAAA
* *
26074 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTAAAAGAT
** * *
26104 TTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAA
1 TTTTGTTTCAAAAGAAACAAAC-T-AAA-AG----AT
* *
26141 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTAAAAGAT
** * *
26171 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TAA-A-AG----AT
* *
26208 TTTTGTTTCCAAAGAAACAAACTTAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTAAAAGAT
** * *
26238 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TAA-A-AG----AT
* *
26275 TTTTGTTTCCAAAGAAACAAACTTAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTAAAAGAT
* *
26305 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTAAAAGAT
26335 TTTT
1 TTTT
26339 TTAACAAAAT
Statistics
Matches: 175, Mismatches: 39, Indels: 42
0.68 0.15 0.16
Matches are distributed among these distances:
30 88 0.50
31 5 0.03
32 4 0.02
33 6 0.03
34 6 0.03
35 4 0.02
36 5 0.03
37 57 0.33
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTAAAAGAT
Found at i:26128 original size:67 final size:67
Alignment explanation
Indices: 26022--26321 Score: 525
Period size: 67 Copynumber: 4.5 Consensus size: 67
26012 TCATTTTAAG
* * *
26022 AGAAACAGATTCAAAGA--TTT-TTTCAAAAGAAATTGTCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
26084 AA
66 AA
*
26086 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
26151 AA
66 AA
26153 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
26218 AA
66 AA
*
26220 AGAAACAAACTTAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
26285 AA
66 AA
*
26287 AGAAACAAACTTAAAGATTTTTGTTTCAAAAGAAA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
26322 CAATCTCAAA
Statistics
Matches: 227, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
64 15 0.07
66 3 0.01
67 209 0.92
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:26347 original size:30 final size:30
Alignment explanation
Indices: 26275--26347 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
26265 AGAGACAAAA
* * *
26275 TTTTGTTTCCAAAGAAACAAACTTAAAGAT
1 TTTTGTTACAAAAGAAACAAACTCAAAGAT
* *
26305 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTACAAAAGAAACAAACTCAAAGAT
26335 TTTT-TTAACAAAA
1 TTTTGTT-ACAAAA
26348 TTGTCTCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 2 0.05
30 36 0.95
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (30 bp):
TTTTGTTACAAAAGAAACAAACTCAAAGAT
Found at i:26472 original size:25 final size:25
Alignment explanation
Indices: 26425--26518 Score: 89
Period size: 27 Copynumber: 3.5 Consensus size: 25
26415 CAAAACTTTG
* *
26425 TTTCAAAATAAATAGACTCAAAGATT
1 TTTCAAAAGAAACA-ACTCAAAGATT
26451 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAG--ATT
* *
26478 TATTCAAAAGGAACAAACTCCAAGATTT
1 T-TTCAAAAGAAAC-AACTCAAAGA-TT
*
26506 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
26519 TGTCTCAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
25 8 0.14
26 12 0.21
27 15 0.26
28 14 0.25
29 8 0.14
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (25 bp):
TTTCAAAAGAAACAACTCAAAGATT
Found at i:26602 original size:28 final size:27
Alignment explanation
Indices: 26557--26863 Score: 107
Period size: 28 Copynumber: 10.5 Consensus size: 27
26547 AAATAAATAG
*
26557 ACTCACAGATTTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGAAACAA
*
26583 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGAAACAA
* *
26612 ACTCCAAGATTTTTTTCAAGAGAAACTGTCTCAAGA
1 ACTCAAAGA-TTTTTTCAAAAGAAA------C-A-A
* * ** * * * *
26648 GACACAAAAATCGTTTTAAAATAAATAG
1 -ACTCAAAGATTTTTTCAAAAGAAACAA
* *
26676 ACTCACAGATTTTTTTAAAAGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGAAACAA
*
26702 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGAAACAA
* *
26731 ACTCCAAGATTTTTTTCAAGAGAAACTGTCTCAAGA
1 ACTCAAAGA-TTTTTTCAAAAGAAA------C-A-A
* * ** * * * *
26767 GACACAAAAATCGTTTTAAAATAAATAG
1 -ACTCAAAGATTTTTTCAAAAGAAACAA
*
26795 ACTCACAGATTTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTCAAAAGAAACAA
*
26821 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTT-TTCAAAAGAAACAA
*
26850 ACTCCAAGATTTTT
1 ACTCAAAGATTTTT
26864 ATTCACGAGA
Statistics
Matches: 201, Mismatches: 51, Indels: 57
0.65 0.17 0.18
Matches are distributed among these distances:
26 27 0.13
27 45 0.22
28 53 0.26
29 36 0.18
30 2 0.01
34 2 0.01
35 2 0.01
36 22 0.11
37 12 0.06
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (27 bp):
ACTCAAAGATTTTTTCAAAAGAAACAA
Found at i:26681 original size:119 final size:119
Alignment explanation
Indices: 26396--26909 Score: 879
Period size: 119 Copynumber: 4.3 Consensus size: 119
26386 GATCTTTCAC
* * * * * *
26396 GAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGACTCAAAGA-TTTTTCAAAAG
1 GAAACTGTCTCAAGAGACACAAAA-ATCGTTTTAAAATAAATAGACTCACAGATTTTTTCAAAAG
26460 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGA-TTTTTTCAAGA
65 AAACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTTTCAAGA
26514 GAAACTGTCTCAAGAGACACAAAAATCGTTTTAAAATAAATAGACTCACAGATTTTTTCAAAAGA
1 GAAACTGTCTCAAGAGACACAAAAATCGTTTTAAAATAAATAGACTCACAGATTTTTTCAAAAGA
26579 AACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTTTCAAGA
66 AACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTTTCAAGA
*
26633 GAAACTGTCTCAAGAGACACAAAAATCGTTTTAAAATAAATAGACTCACAGATTTTTTTAAAAGA
1 GAAACTGTCTCAAGAGACACAAAAATCGTTTTAAAATAAATAGACTCACAGATTTTTTCAAAAGA
26698 AACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTTTCAAGA
66 AACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTTTCAAGA
26752 GAAACTGTCTCAAGAGACACAAAAATCGTTTTAAAATAAATAGACTCACAGATTTTTTCAAAAGA
1 GAAACTGTCTCAAGAGACACAAAAATCGTTTTAAAATAAATAGACTCACAGATTTTTTCAAAAGA
*
26817 AACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTCACGA
66 AACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTT-TTCAAGA
* * *
26872 GAAACTGTCTTTAAGAGATAAAAAAAATCGTTTTAAAA
1 GAAACTGTC-TCAAGAGA-CACAAAAATCGTTTTAAAA
26910 GATTCAAATA
Statistics
Matches: 379, Mismatches: 12, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
117 24 0.06
118 76 0.20
119 240 0.63
120 15 0.04
121 7 0.02
122 17 0.04
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.27
Consensus pattern (119 bp):
GAAACTGTCTCAAGAGACACAAAAATCGTTTTAAAATAAATAGACTCACAGATTTTTTCAAAAGA
AACAACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTTTTCAAGA
Found at i:26853 original size:29 final size:27
Alignment explanation
Indices: 26795--26868 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 27
26785 AAATAAATAG
*
26795 ACTCACAGATTTT-TTCAAAAGAAACA
1 ACTCAAAGATTTTATTCAAAAGAAACA
*
26821 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTTATTCAAAAGAAAC-A
*
26850 ACTCCAAGATTTTTATTCA
1 ACTCAAAGA-TTTTATTCA
26869 CGAGAAACTG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.22
27 3 0.07
28 11 0.27
29 17 0.41
30 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.08, T:0.30
Consensus pattern (27 bp):
ACTCAAAGATTTTATTCAAAAGAAACA
Found at i:27248 original size:36 final size:36
Alignment explanation
Indices: 27152--27236 Score: 118
Period size: 36 Copynumber: 2.4 Consensus size: 36
27142 TTAAGATATA
* *
27152 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAT
* *
27188 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAT
27223 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
27237 TCAACTTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 8 0.19
36 35 0.81
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAT
Found at i:27367 original size:105 final size:101
Alignment explanation
Indices: 27188--27420 Score: 283
Period size: 105 Copynumber: 2.3 Consensus size: 101
27178 TAGAGAAATT
*
27188 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAATGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAAAGATCTCAAGTGAGATCAACTTTGTTTAAT
* *
27252 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
27290 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAAGAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AGAAA-AAG-ATCTCAA-GTGAGATCAACTTTGTTT
* * * *
27354 -TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AAT-GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
27395 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
27421 AAAATTTTCA
Statistics
Matches: 114, Mismatches: 10, Indels: 11
0.84 0.07 0.08
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 8 0.07
104 5 0.04
105 78 0.68
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAAAGATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:27488 original size:38 final size:38
Alignment explanation
Indices: 27446--27581 Score: 123
Period size: 38 Copynumber: 3.8 Consensus size: 38
27436 TGTGGAAAAA
*
27446 TGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGT
* * **
27484 TGTCT-AATTC---TCAAAATTTG---T---G-GAAAAA
1 TGTCTCAA-GCGAGACAAAATTTGTTTTAAAGAGAAAGT
*
27512 TGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGT
*
27550 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGA
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAAGA
27582 AAACTGTCTC
Statistics
Matches: 74, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
28 10 0.14
29 3 0.04
31 8 0.11
32 1 0.01
34 1 0.01
35 8 0.11
37 3 0.04
38 40 0.54
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (38 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAAGAGAAAGT
Found at i:27509 original size:66 final size:66
Alignment explanation
Indices: 27423--27554 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
27413 TTTGTTTTAA
*
27423 AATTTTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
1 AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
27488 T
66 T
27489 AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
1 AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
27554 T
66 T
27555 CAAGCGAGAC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (66 bp):
AATTCTCAAAATTTGTGGAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAAGAGAAAGTTGTC
T
Found at i:27573 original size:21 final size:21
Alignment explanation
Indices: 27512--27573 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
27502 TGTGGAAAAA
*
27512 TGTCTCAAGCGAGACATAATT
1 TGTCTCAAGCGAGACAAAATT
* * * *
27533 TGTTTTAA---AGA-GAAAGT
1 TGTCTCAAGCGAGACAAAATT
27550 TGTCTCAAGCGAGACAAAATT
1 TGTCTCAAGCGAGACAAAATT
27571 TGT
1 TGT
27574 TTTTAAGAAA
Statistics
Matches: 28, Mismatches: 9, Indels: 8
0.62 0.20 0.18
Matches are distributed among these distances:
17 9 0.32
18 3 0.11
20 3 0.11
21 13 0.46
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (21 bp):
TGTCTCAAGCGAGACAAAATT
Found at i:27590 original size:36 final size:36
Alignment explanation
Indices: 27506--27614 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 36
27496 AAAATTTGTG
* *
27506 GAAAAATGTCTCAAGCGAGACATAATTTGTTTTAAA
1 GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
*
27542 GAGAAAGTTGTCTCAAGCGAGACAAAATTTGTTTTTAA
1 GA-AAA-ATGTCTCAAGCGAGACAAAATTTGTTTTTAA
* * * * *
27580 GAAAACTGTCTCTAGTGAGACGACACTTTGTTTTT
1 GAAAAATGTCTCAAGCGAGAC-AAAATTTGTTTTT
27615 TTTTTTTTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
36 15 0.24
37 17 0.27
38 30 0.48
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
GAAAAATGTCTCAAGCGAGACAAAATTTGTTTTTAA
Found at i:27965 original size:4 final size:4
Alignment explanation
Indices: 27956--28013 Score: 77
Period size: 4 Copynumber: 15.0 Consensus size: 4
27946 TTTATGTATC
*
27956 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
28002 AT-T GATGT ATGT
1 ATGT -ATGT ATGT
28014 TTTTCTCGAG
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 2 0.04
3 1 0.02
4 44 0.92
5 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:29216 original size:12 final size:11
Alignment explanation
Indices: 29188--29228 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
29178 TCCTCTTTTG
*
29188 TTCTTTGCTTT
1 TTCTTTGATTT
29199 TTCTTTGATTT
1 TTCTTTGATTT
29210 TTGCTTTGATTT
1 TT-CTTTGATTT
29222 TCTCTTT
1 T-TCTTT
29229 TCTCTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 12 0.44
12 14 0.52
13 1 0.04
ACGTcount: A:0.05, C:0.15, G:0.10, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:29258 original size:30 final size:30
Alignment explanation
Indices: 29195--29258 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
29185 TTGTTCTTTG
**
29195 CTTTTTCTTTGATTTTTGCTTTGATTTTCT
1 CTTTTTCTTTGATTTTTGCTTTGATTTGAT
* *
29225 CTTTTCTCTTTG-TTTTTTCTTTGGTTTGAT
1 CTTTT-TCTTTGATTTTTGCTTTGATTTGAT
29255 CTTT
1 CTTT
29259 GCACTCTGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 23 0.79
31 6 0.21
ACGTcount: A:0.05, C:0.14, G:0.11, T:0.70
Consensus pattern (30 bp):
CTTTTTCTTTGATTTTTGCTTTGATTTGAT
Found at i:29921 original size:46 final size:45
Alignment explanation
Indices: 29829--29922 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 45
29819 ATAAATGCAG
* * * *
29829 TGTTTCAAGGTGGAAAGAATGTTTCAAGGCCTTAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
* *
29874 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
29920 TGT
1 TGT
29923 CAAAAATTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
Found at i:35826 original size:3 final size:3
Alignment explanation
Indices: 35818--35872 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
35808 GGCCTGCAAA
*
35818 AAT AAT AAT AAT AAT AATT AAT AA- ACAT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT A-AT AAT AAT AAT AAT AAT AAT
35864 AAT AAT AAT
1 AAT AAT AAT
35873 TAAAATTAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:37097 original size:2 final size:2
Alignment explanation
Indices: 37090--37117 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37080 GAAACATCTT
37090 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
37118 GAGTCTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:46383 original size:26 final size:26
Alignment explanation
Indices: 46349--46401 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
46339 TTTAAGAATA
46349 TATTATCCAAATCAAACAATGATAAT
1 TATTATCCAAATCAAACAATGATAAT
46375 TATTATCCAAATCAAACAATGATAAT
1 TATTATCCAAATCAAACAATGATAAT
46401 T
1 T
46402 TAAATTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (26 bp):
TATTATCCAAATCAAACAATGATAAT
Found at i:48808 original size:21 final size:23
Alignment explanation
Indices: 48784--48827 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
48774 AATAATCTAA
*
48784 ATTAATTTAA-TTTA-AGAATAT
1 ATTAATATAATTTTATAGAATAT
48805 ATTAATATAATTTTATAGAATAT
1 ATTAATATAATTTTATAGAATAT
48828 GATTGGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTAATATAATTTTATAGAATAT
Found at i:51309 original size:19 final size:20
Alignment explanation
Indices: 51281--51324 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
51271 AATTTAAAAA
*
51281 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
51300 TAAATAATATTAGAATAATT
1 TAAATAATATAAAAATAATT
51320 TAAAT
1 TAAAT
51325 TTTTTATGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:51653 original size:25 final size:25
Alignment explanation
Indices: 51608--51655 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
51598 TAAAAATTAT
* *
51608 ATAAATTAATTAATATAATTTAAGA
1 ATAAATTAATAAAAATAATTTAAGA
51633 ATAAATTATATAAAAAT-ATTTAA
1 ATAAATTA-ATAAAAATAATTTAA
51656 ATAATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATAAATTAATAAAAATAATTTAAGA
Found at i:51662 original size:19 final size:20
Alignment explanation
Indices: 51634--51677 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
51624 AATTTAAGAA
*
51634 TAAATTATATAAAAAT-ATT
1 TAAATAATATAAAAATAATT
* *
51653 TAAATAATATTATAATAATT
1 TAAATAATATAAAAATAATT
51673 TAAAT
1 TAAAT
51678 CAATTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAATAATATAAAAATAATT
Found at i:51720 original size:13 final size:14
Alignment explanation
Indices: 51702--51730 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
51692 AATATACTAA
51702 TATAATTTAAA-AT
1 TATAATTTAAATAT
51715 TATAATTTAAATAT
1 TATAATTTAAATAT
51729 TA
1 TA
51731 ATATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TATAATTTAAATAT
Found at i:52003 original size:21 final size:20
Alignment explanation
Indices: 51977--52030 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
51967 TTTATAAATT
51977 AATTAATTTAAATTAAGAATA
1 AATTAATTTAAATTAAG-ATA
* *
51998 AATTAATTTAATTTATGATA
1 AATTAATTTAAATTAAGATA
**
52018 TTTTAATTTAAAT
1 AATTAATTTAAAT
52031 AAATTATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (20 bp):
AATTAATTTAAATTAAGATA
Found at i:56063 original size:15 final size:17
Alignment explanation
Indices: 56039--56075 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
56029 TAATCTGATC
*
56039 CAAATGTAAAAA-AATT
1 CAAATATAAAAATAATT
56055 -AAATATAAAAATAATT
1 CAAATATAAAAATAATT
56071 CAAAT
1 CAAAT
56076 GCATTGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (17 bp):
CAAATATAAAAATAATT
Found at i:56881 original size:26 final size:25
Alignment explanation
Indices: 56817--56881 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 25
56807 AAATAGCATA
* *
56817 AAATCAAA-ATTCATATCATAGTCC
1 AAATCAAACATTAATATCATAATCC
* * * *
56841 ATATCAACCAATAATAATCGTAATCC
1 AAATCAAACATTAAT-ATCATAATCC
56867 AAATCAAACATTAAT
1 AAATCAAACATTAAT
56882 CAGTCCTAAT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
24 6 0.20
25 4 0.13
26 20 0.67
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.28
Consensus pattern (25 bp):
AAATCAAACATTAATATCATAATCC
Found at i:58335 original size:21 final size:22
Alignment explanation
Indices: 58309--58353 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
58299 GATAATTTAA
* *
58309 ATTAATTTCATTT-AAGAATAT
1 ATTAATATAATTTAAAGAATAT
*
58330 ATTAATATAATTTAAATAATAT
1 ATTAATATAATTTAAAGAATAT
58352 AT
1 AT
58354 CTTATGATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTAATATAATTTAAAGAATAT
Found at i:62094 original size:15 final size:15
Alignment explanation
Indices: 62074--62102 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
62064 GTTCTTACTG
62074 AAACTGCTCACTGCA
1 AAACTGCTCACTGCA
62089 AAACTGCTCACTGC
1 AAACTGCTCACTGC
62103 GTCTGTTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.34, G:0.14, T:0.21
Consensus pattern (15 bp):
AAACTGCTCACTGCA
Found at i:63092 original size:14 final size:14
Alignment explanation
Indices: 63073--63105 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
63063 CACATATATA
63073 ATAATTTATAGTTT
1 ATAATTTATAGTTT
63087 ATAATTTATAGTTT
1 ATAATTTATAGTTT
63101 A-AATT
1 ATAATT
63106 AATATTATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
ATAATTTATAGTTT
Found at i:63291 original size:21 final size:23
Alignment explanation
Indices: 63267--63310 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
63257 AATAATCTAA
*
63267 ATTAATTTAA-TTTA-AGAATAT
1 ATTAATATAATTTTATAGAATAT
63288 ATTAATATAATTTTATAGAATAT
1 ATTAATATAATTTTATAGAATAT
63311 GATTGGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTAATATAATTTTATAGAATAT
Found at i:65805 original size:21 final size:22
Alignment explanation
Indices: 65709--65805 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 22
65699 AACTATAAAC
*
65709 ATATAATTTAAGAATA-AATTA
1 ATATAATTTAAGAATATATTTA
*
65730 ATTTAATTTAA-AA-ATATTTA
1 ATATAATTTAAGAATATATTTA
65750 A-ATAATATT-AGAATA-ATTTAA
1 ATATAAT-TTAAGAATATATTT-A
* *
65771 ATTATTTATGTTAAGAACATA-TTA
1 A-TA-TAAT-TTAAGAATATATTTA
65795 ATATAATTTAA
1 ATATAATTTAA
65806 ATCTATAATT
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
19 6 0.10
20 15 0.25
21 17 0.29
22 3 0.05
23 3 0.05
24 7 0.12
25 7 0.12
26 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATAATTTAAGAATATATTTA
Found at i:65814 original size:13 final size:13
Alignment explanation
Indices: 65796--65820 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65786 AACATATTAA
65796 TATAATTTAAATC
1 TATAATTTAAATC
65809 TATAATTTAAAT
1 TATAATTTAAAT
65821 ATTAATATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATTTAAATC
Done.