Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008181.1 Hibiscus syriacus cultivar Beakdansim tig00110781_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: 428138
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:270726 original size:24 final size:24
Alignment explanation
Indices: 270656--270726 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 24
270646 TGAGTAAGAG
*
270656 AGAGAAAAAGTAAAAGTTAACATGAA
1 AGAGAAAAA-AAAAAGTTAA-ATGAA
* *
270682 AGAGAAAAAAAAATGAATAAA-GAA
1 AGAGAAAAAAAAAAG-TTAAATGAA
270706 AGAGAAAAGAAAAAAGTTAAA
1 AGAGAAAA-AAAAAAGTTAAA
270727 AATTTGGGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 15 0.39
25 11 0.29
26 12 0.32
ACGTcount: A:0.69, C:0.01, G:0.18, T:0.11
Consensus pattern (24 bp):
AGAGAAAAAAAAAAGTTAAATGAA
Found at i:277616 original size:24 final size:24
Alignment explanation
Indices: 277572--277621 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
277562 ATAAAGAACC
*
277572 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
277596 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
277620 AA
1 AA
277622 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:288850 original size:27 final size:27
Alignment explanation
Indices: 288809--288861 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
288799 TATTTTCACG
288809 GGATCTCTGACCATGACCGAGAAATCT
1 GGATCTCTGACCATGACCGAGAAATCT
*
288836 GGATCTCTGATCATGACCGAGAAATC
1 GGATCTCTGACCATGACCGAGAAATC
288862 CGCCTGGATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (27 bp):
GGATCTCTGACCATGACCGAGAAATCT
Found at i:294739 original size:15 final size:16
Alignment explanation
Indices: 294706--294739 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
294696 TATGTTGTGA
*
294706 GTTCTAGAATAGTTTT
1 GTTCTAGAATAGATTT
294722 GTTCTAGAATA-ATTT
1 GTTCTAGAATAGATTT
294737 GTT
1 GTT
294740 AGCTTGTAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (16 bp):
GTTCTAGAATAGATTT
Found at i:300489 original size:29 final size:29
Alignment explanation
Indices: 300452--300511 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
300442 TTTCATAATT
*
300452 TTTCT-AAAAATTAAATAAGTCCTCAAAC
1 TTTCTAAAAAATCAAATAAGTCCTCAAAC
* *
300480 TTTCTAAAAAAATCAATTATGTCCTCAAAC
1 TTTCT-AAAAAATCAAATAAGTCCTCAAAC
300510 TT
1 TT
300512 AGCAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 5 0.19
30 22 0.81
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.35
Consensus pattern (29 bp):
TTTCTAAAAAATCAAATAAGTCCTCAAAC
Found at i:300498 original size:34 final size:32
Alignment explanation
Indices: 300460--300529 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 32
300450 TTTTTCTAAA
* *
300460 AATTAAATAAGTCCTCAAACTT-TCTAAAAAAATC
1 AATTAAAT--GTCCTCAAACTTAGC-AAAAAAAAC
300494 AATT--ATGTCCTCAAACTTAGCAAAAAAAAC
1 AATTAAATGTCCTCAAACTTAGCAAAAAAAAC
300524 AATTAA
1 AATTAA
300530 GCTTATCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
30 24 0.77
31 1 0.03
32 2 0.06
34 4 0.13
ACGTcount: A:0.51, C:0.17, G:0.04, T:0.27
Consensus pattern (32 bp):
AATTAAATGTCCTCAAACTTAGCAAAAAAAAC
Found at i:300504 original size:30 final size:30
Alignment explanation
Indices: 300470--300528 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
300460 AATTAAATAA
* *
300470 GTCCTCAAACTT-TCTAAAAAAATCAATTAT
1 GTCCTCAAACTTAGC-AAAAAAAACAATTAT
300500 GTCCTCAAACTTAGCAAAAAAAACAATTA
1 GTCCTCAAACTTAGCAAAAAAAACAATTA
300529 AGCTTATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.27
Consensus pattern (30 bp):
GTCCTCAAACTTAGCAAAAAAAACAATTAT
Found at i:300625 original size:21 final size:21
Alignment explanation
Indices: 300601--300643 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
300591 CAATTTTGTA
* *
300601 AATTTTCATGTAAGCTTCGTG
1 AATTGTCATGTAAGCGTCGTG
300622 AATTGTCATGTAAGCGTCGTG
1 AATTGTCATGTAAGCGTCGTG
300643 A
1 A
300644 CAGTCAACGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (21 bp):
AATTGTCATGTAAGCGTCGTG
Found at i:306514 original size:15 final size:16
Alignment explanation
Indices: 306494--306523 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
306484 AAAAGTTTTA
306494 TTATTTTAA-TAAAAT
1 TTATTTTAAGTAAAAT
306509 TTATTTTAAGTAAAA
1 TTATTTTAAGTAAAA
306524 GGTATTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTATTTTAAGTAAAAT
Found at i:312917 original size:12 final size:12
Alignment explanation
Indices: 312897--312984 Score: 56
Period size: 12 Copynumber: 6.9 Consensus size: 12
312887 TTTGCCAGTT
*
312897 TATAATATTATA
1 TATATTATTATA
312909 TATATTATTAACTA
1 TATATTATT-A-TA
*
312923 TATATATTTTATTA
1 TATAT-TATTA-TA
312937 TATACGTTATTAT-
1 TATA--TTATTATA
*
312950 TATA-TATAATA
1 TATATTATTATA
312961 TATTATTATTAT-
1 TA-TATTATTATA
312973 TATTATTATTAT
1 TA-TATTATTAT
312985 TATTAAATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.08
11 2 0.03
12 22 0.35
13 10 0.16
14 15 0.24
15 7 0.11
16 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (12 bp):
TATATTATTATA
Found at i:312949 original size:3 final size:3
Alignment explanation
Indices: 312943--312989 Score: 67
Period size: 3 Copynumber: 15.0 Consensus size: 3
312933 ATTATATACG
*
312943 TTA TTA TTA TATA TAA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
312990 AATAATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:314309 original size:26 final size:25
Alignment explanation
Indices: 314278--314343 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
314268 ATTTTAAGAC
314278 TAATTATAATATTAGTATAAT-TATA
1 TAATTATAATATTA-TATAATCTATA
*
314303 TATATTATGATAACTT-TATAATCTATA
1 TA-ATTATAAT-A-TTATATAATCTATA
*
314330 TAATTTTAATATTA
1 TAATTATAATATTA
314344 AATATTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
24 2 0.06
25 3 0.09
26 19 0.58
27 7 0.21
28 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (25 bp):
TAATTATAATATTATATAATCTATA
Found at i:314315 original size:18 final size:18
Alignment explanation
Indices: 314260--314343 Score: 56
Period size: 18 Copynumber: 4.8 Consensus size: 18
314250 TTTTCATCAT
* *
314260 TAATTAT-TATTTTAAGA
1 TAATTATATATATTATGA
314277 CTAATTATA-ATATTA-GTA
1 -TAATTATATATATTATG-A
314295 TAATTATATATATTATGA
1 TAATTATATATATTATGA
314313 TAACTT-TATA-ATCTAT-A
1 TAA-TTATATATAT-TATGA
*
314330 TAATTTTA-ATATTA
1 TAATTATATATATTA
314344 AATATTATAA
Statistics
Matches: 57, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
16 5 0.09
17 19 0.33
18 30 0.53
19 3 0.05
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (18 bp):
TAATTATATATATTATGA
Found at i:320420 original size:5 final size:5
Alignment explanation
Indices: 320406--320437 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
320396 AAAAAAAAAT
320406 TCGGG TTCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG -TCGGG TCGGG TCGGG TCGGG TCGGG T
320438 TTAGGGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.19, G:0.56, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:321121 original size:55 final size:56
Alignment explanation
Indices: 321048--321155 Score: 173
Period size: 55 Copynumber: 1.9 Consensus size: 56
321038 CTTATTCGAG
* *
321048 ATTTGATTAAGATGTGGAGACATGAAATGAATTAAGATGAATCCTTCTTGTGAATT
1 ATTTGATTAAGATGTGGAGACATGAAAGGAATTAAGATAAATCCTTCTTGTGAATT
* *
321104 ATTTGATT-AGATGTGGAGACATGAAAGGAATTAGGATAAATCCTTTTTGTGA
1 ATTTGATTAAGATGTGGAGACATGAAAGGAATTAAGATAAATCCTTCTTGTGA
321156 TGTGTTCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
55 40 0.83
56 8 0.17
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (56 bp):
ATTTGATTAAGATGTGGAGACATGAAAGGAATTAAGATAAATCCTTCTTGTGAATT
Found at i:321906 original size:41 final size:41
Alignment explanation
Indices: 321849--321951 Score: 145
Period size: 41 Copynumber: 2.5 Consensus size: 41
321839 TCACGAATTT
*
321849 TTAAATCCTTCGGGTCATCTGTAAGTCCTTCGAG-CATGATG
1 TTAAATCCTTAGGGTCATCTGTAAGTCCTTCGAGCCA-GATG
* * *
321890 TTAAAACCTTAGGGTCATCTGTCAGTCTTTCGAGCCAGATG
1 TTAAATCCTTAGGGTCATCTGTAAGTCCTTCGAGCCAGATG
*
321931 ATAAATCCTTAGGGTCATCTG
1 TTAAATCCTTAGGGTCATCTG
321952 CCAAACCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 53 0.96
42 2 0.04
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.33
Consensus pattern (41 bp):
TTAAATCCTTAGGGTCATCTGTAAGTCCTTCGAGCCAGATG
Found at i:322021 original size:18 final size:19
Alignment explanation
Indices: 321981--322022 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
321971 TTGGCTCACA
321981 GAATGTAAGATTACCAGAGG
1 GAATGTAAGATTACCA-AGG
*
322001 GAATGTAATATTACC-AGG
1 GAATGTAAGATTACCAAGG
322019 GAAT
1 GAAT
322023 AGGATTACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (19 bp):
GAATGTAAGATTACCAAGG
Found at i:322246 original size:37 final size:37
Alignment explanation
Indices: 322173--322247 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
322163 GTTGGAAAAT
*
322173 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
322210 ATTTATATACTTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTAAAAAAATT-AAAATCATAAA
322247 A
1 A
322248 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 25 0.76
38 8 0.24
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:329802 original size:16 final size:16
Alignment explanation
Indices: 329772--329802 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
329762 TAATATTGAA
*
329772 ACTTGAACTCAAAAAG
1 ACTTGAACTAAAAAAG
329788 ACTTGAACTAAAAAA
1 ACTTGAACTAAAAAA
329803 AAAATTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTAAAAAAG
Found at i:331908 original size:23 final size:23
Alignment explanation
Indices: 331882--331926 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
331872 TGTGTTTTCT
331882 TTTTAAAAATATATATAATTTTA
1 TTTTAAAAATATATATAATTTTA
* * *
331905 TTTTTAAATTTTATATAATTTT
1 TTTTAAAAATATATATAATTTT
331927 TTAAAATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTAAAAATATATATAATTTTA
Found at i:334271 original size:21 final size:21
Alignment explanation
Indices: 334247--334286 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
334237 TATTTTATCC
*
334247 GAACTCGACGAGTTATAATCT
1 GAACTCGACAAGTTATAATCT
*
334268 GAACTCGATAAGTTATAAT
1 GAACTCGACAAGTTATAAT
334287 GAAAAGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
GAACTCGACAAGTTATAATCT
Found at i:334673 original size:14 final size:14
Alignment explanation
Indices: 334654--334680 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
334644 TTTTTTAAGT
334654 TTGAGTTATTTAAA
1 TTGAGTTATTTAAA
334668 TTGAGTTATTTAA
1 TTGAGTTATTTAA
334681 CTCAACTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (14 bp):
TTGAGTTATTTAAA
Found at i:335287 original size:21 final size:23
Alignment explanation
Indices: 335263--335308 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
335253 TCATAAAAAT
335263 AATTTT-TAA-ATACAAAAGTAA
1 AATTTTCTAATATACAAAAGTAA
* *
335284 AATTTTCTAATATTCAGAAGTAA
1 AATTTTCTAATATACAAAAGTAA
335307 AA
1 AA
335309 CAAATTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 12 0.57
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.35
Consensus pattern (23 bp):
AATTTTCTAATATACAAAAGTAA
Found at i:335943 original size:31 final size:31
Alignment explanation
Indices: 335865--335949 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
335855 GGAATGCCTT
*
335865 GGGGCCCGAGAGCCTACCCAAGAAAGTTACTC
1 GGGGCCC-AGAGCCTACCCAAGAAAGATACTC
* *
335897 AGGG-CCACGAGGCCTACCCAAGAATGAT-CTC
1 GGGGCCCA-GA-GCCTACCCAAGAAAGATACTC
*
335928 GGGGCCTCAGAGCCTATCCAAG
1 GGGGCC-CAGAGCCTACCCAAG
335950 GGTTGTCTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
30 1 0.02
31 20 0.45
32 21 0.48
33 2 0.05
ACGTcount: A:0.27, C:0.32, G:0.28, T:0.13
Consensus pattern (31 bp):
GGGGCCCAGAGCCTACCCAAGAAAGATACTC
Found at i:338392 original size:22 final size:22
Alignment explanation
Indices: 338364--338417 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
338354 CAGTTAACGA
338364 TCAGACCGGTCAAAGTCAACAG
1 TCAGACCGGTCAAAGTCAACAG
* *
338386 TCAGACCGATCAAAGTCAACGG
1 TCAGACCGGTCAAAGTCAACAG
338408 TCAGACCGGT
1 TCAGACCGGT
338418 AAACGGGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (22 bp):
TCAGACCGGTCAAAGTCAACAG
Found at i:338459 original size:13 final size:13
Alignment explanation
Indices: 338441--338467 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
338431 CAGTCAAGTC
338441 AATGAGTTGACTT
1 AATGAGTTGACTT
338454 AATGAGTTGACTT
1 AATGAGTTGACTT
338467 A
1 A
338468 GCCGAGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (13 bp):
AATGAGTTGACTT
Found at i:345921 original size:18 final size:18
Alignment explanation
Indices: 345898--345932 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
345888 TTAGCGTTGT
345898 GAAAAG-AAAATAATGAAA
1 GAAAAGTAAAA-AATGAAA
345916 GAAAAGTAAAAAATGAA
1 GAAAAGTAAAAAATGAA
345933 GGGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (18 bp):
GAAAAGTAAAAAATGAAA
Found at i:351431 original size:6 final size:6
Alignment explanation
Indices: 351420--351450 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
351410 TCTTTCAACT
351420 ACTTCC ACTTCC ACTTCC ACTTCC ACTTCC A
1 ACTTCC ACTTCC ACTTCC ACTTCC ACTTCC A
351451 TTTAATCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.32
Consensus pattern (6 bp):
ACTTCC
Found at i:352044 original size:28 final size:29
Alignment explanation
Indices: 352012--352072 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
352002 TATGACTCTC
352012 ATTTTAAATT-AGTCACTAAA-TTTTGAAT
1 ATTTTAAATTCAGTCAC-AAATTTTTGAAT
* * *
352040 ATTTTAATTTCATTCTCAAATTTTTGAAT
1 ATTTTAAATTCAGTCACAAATTTTTGAAT
352069 ATTT
1 ATTT
352073 CAATTTTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.52
Consensus pattern (29 bp):
ATTTTAAATTCAGTCACAAATTTTTGAAT
Found at i:352087 original size:28 final size:29
Alignment explanation
Indices: 352032--352087 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
352022 AGTCACTAAA
* *
352032 TTTTGAATATTTTAATTTCATTCTCAAAT
1 TTTTGAATATTTCAATTTCATTCCCAAAT
*
352061 TTTTGAATATTTCAATTTTA-TCCCAAA
1 TTTTGAATATTTCAATTTCATTCCCAAA
352088 CTATAGGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTTGAATATTTCAATTTCATTCCCAAAT
Found at i:352257 original size:29 final size:29
Alignment explanation
Indices: 352210--352287 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
352200 TAAATTTGCG
352210 GATGAAATTGAAAGATTCAAAAGTTTAGA
1 GATGAAATTGAAAGATTCAAAAGTTTAGA
* * * * *
352239 GATGAATTTGGAAGCTTCAAAAGTTTTGG
1 GATGAAATTGAAAGATTCAAAAGTTTAGA
* *
352268 GATGAAATTAAAATATTCAA
1 GATGAAATTGAAAGATTCAA
352288 GAATTTAAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (29 bp):
GATGAAATTGAAAGATTCAAAAGTTTAGA
Found at i:352421 original size:40 final size:40
Alignment explanation
Indices: 352366--352449 Score: 159
Period size: 40 Copynumber: 2.1 Consensus size: 40
352356 AATCATATAC
*
352366 ATATGATGTAGTTAACCCTATCTAATATTTAATTAATAAA
1 ATATGATGTAGTTAACCCTATCAAATATTTAATTAATAAA
352406 ATATGATGTAGTTAACCCTATCAAATATTTAATTAATAAA
1 ATATGATGTAGTTAACCCTATCAAATATTTAATTAATAAA
352446 ATAT
1 ATAT
352450 TATAAATCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (40 bp):
ATATGATGTAGTTAACCCTATCAAATATTTAATTAATAAA
Found at i:353144 original size:30 final size:30
Alignment explanation
Indices: 353110--353182 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
353100 AAGCAGAAGC
353110 AGAAGCAGGAGTAGAGAGACAAGGAGACGA
1 AGAAGCAGGAGTAGAGAGACAAGGAGACGA
* * *
353140 AGAAGCAGGAGTAGAGAGAGAAGGAGGCGG
1 AGAAGCAGGAGTAGAGAGACAAGGAGACGA
353170 AGAAGCAGGAGTA
1 AGAAGCAGGAGTA
353183 CGAGTAGGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.44, C:0.08, G:0.44, T:0.04
Consensus pattern (30 bp):
AGAAGCAGGAGTAGAGAGACAAGGAGACGA
Found at i:358645 original size:11 final size:11
Alignment explanation
Indices: 358629--358659 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
358619 CATTTCGACC
358629 AAAAAAATAAA
1 AAAAAAATAAA
*
358640 AAAAAAATAAT
1 AAAAAAATAAA
358651 AAAAAAATA
1 AAAAAAATA
358660 TATGGGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (11 bp):
AAAAAAATAAA
Found at i:372245 original size:221 final size:222
Alignment explanation
Indices: 371862--372304 Score: 809
Period size: 221 Copynumber: 2.0 Consensus size: 222
371852 CTAGAGTTTC
371862 TAGATATTATTCAGAGATATTGGATAATCTTATCGGGTAGAGAAACACGGATCTTTAGTATACCG
1 TAGATATTATTCAGAGATATTGGATAATCTTATCGGGTAGAGAAACACGGATCTTTAGTATACCG
* *
371927 ATAGAATGTCAGAATTTAGAATCACTATCGGAAGAGTTCATTAATTGACGAAATTATCAGTTATT
66 ATAGAATGTCAGAATTTAGAATCACTATCGGAAGAGTTCATTAACTGACGAAATTATCAGTTAAT
*
371992 CAGAATGTGATTTGAGCTGAATATGAAGAAATGAATGTTCATGACATTTACAGTCTGTGTTGATC
131 CAGAATGTGATTTGAGCTGAATAGGAAGAAATGAATGTTCATGACATTTACAGTCTGTGTTGATC
*
372057 TATACAGGTAA-CCCCTCAGACTGATA
196 TATACAGGTAACCCCCTCAGACCGATA
372083 TAGATATTATTCAGAGATATTGGATAATCTTATCGGGTAGAGAAACACGGATCTTTAGTATACCG
1 TAGATATTATTCAGAGATATTGGATAATCTTATCGGGTAGAGAAACACGGATCTTTAGTATACCG
*
372148 ATAGAATGTCATAATTTAGAATCACTATCGGAAGAGTTCATTAACTGACGAAATTATCAGTTAAT
66 ATAGAATGTCAGAATTTAGAATCACTATCGGAAGAGTTCATTAACTGACGAAATTATCAGTTAAT
372213 CAGAATGTGATTTGAGCTG-ATAAGGAAGAAATGAATGTTCATGACATTTACAGTCTGTGTTGAT
131 CAGAATGTGATTTGAGCTGAAT-AGGAAGAAATGAATGTTCATGACATTTACAGTCTGTGTTGAT
*
372277 CTATACGGGTAACCCCCTCAGACCGATA
195 CTATACAGGTAACCCCCTCAGACCGATA
372305 CGGGTAATCC
Statistics
Matches: 214, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
220 2 0.01
221 198 0.93
222 14 0.07
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (222 bp):
TAGATATTATTCAGAGATATTGGATAATCTTATCGGGTAGAGAAACACGGATCTTTAGTATACCG
ATAGAATGTCAGAATTTAGAATCACTATCGGAAGAGTTCATTAACTGACGAAATTATCAGTTAAT
CAGAATGTGATTTGAGCTGAATAGGAAGAAATGAATGTTCATGACATTTACAGTCTGTGTTGATC
TATACAGGTAACCCCCTCAGACCGATA
Found at i:373078 original size:24 final size:24
Alignment explanation
Indices: 373046--373130 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
373036 TATATCAAAA
* * *
373046 ATCAAAACATAATTCAGGTCAGAT
1 ATCATAACATAATCCATGTCAGAT
*
373070 ATCATAACAAAATCCATGTCA-AGT
1 ATCATAACATAATCCATGTCAGA-T
* * * *
373094 ATCAGATCAGAATCCATGTCAGGT
1 ATCATAACATAATCCATGTCAGAT
373118 ATCATAACATAAT
1 ATCATAACATAAT
373131 TAAAATCGGA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
23 1 0.02
24 47 0.98
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.26
Consensus pattern (24 bp):
ATCATAACATAATCCATGTCAGAT
Found at i:374701 original size:20 final size:20
Alignment explanation
Indices: 374676--374726 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
374666 TTTCCCCAAT
*
374676 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
374696 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
374716 TCGCAATGCGA
1 TCGCAATGCGA
374727 TCTGACTATC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:374821 original size:21 final size:21
Alignment explanation
Indices: 374797--374855 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
374787 ACTGTAGACC
*
374797 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACA
**
374818 ATCGCAACGCGA-TAAC-ACA
1 ATCGCAACGCGATTTTCAACA
*
374837 ATCGCAATGCGATTTTCAA
1 ATCGCAACGCGATTTTCAA
374856 GCGCCATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACA
Found at i:375189 original size:19 final size:20
Alignment explanation
Indices: 375165--375212 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
375155 GCGATTCTCT
375165 CGTTGCGATAGTCA-ATTCG
1 CGTTGCGATAGTCATATTCG
*
375184 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATATTCG
*
375204 TGTTGCGAT
1 CGTTGCGAT
375213 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATATTCG
Found at i:375208 original size:20 final size:20
Alignment explanation
Indices: 375165--375222 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
375155 GCGATTCTCT
*
375165 CGTTGCGATAGTCA-ATTCG
1 CGTTGCGATAGTCATTTTCG
375184 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
375204 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
375223 AGAACTATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 14 0.41
20 20 0.59
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:375411 original size:25 final size:24
Alignment explanation
Indices: 375357--375412 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
375347 TGTTTATTAT
* *
375357 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
375381 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
375407 TGTTTT
1 TGTTTT
375413 GTTTTTGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 19 0.70
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.54
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:376544 original size:18 final size:18
Alignment explanation
Indices: 376523--376567 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
376513 TCCACTTCGG
*
376523 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
376541 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
376559 GAGCCATCA
1 GAGCCATCA
376568 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:377074 original size:20 final size:20
Alignment explanation
Indices: 377049--377094 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
377039 TAGTTTACTT
*
377049 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
377069 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
377089 TCGCAA
1 TCGCAA
377095 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:377103 original size:19 final size:20
Alignment explanation
Indices: 377060--377104 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
377050 CGCAACATGA
377060 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
377080 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
377099 AAATGA
1 AAATGA
377105 AAATCACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:377146 original size:19 final size:18
Alignment explanation
Indices: 377088--377151 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
377078 GGAAATGGCT
377088 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
* *
377107 ATCACAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
377121 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
377139 AGTCGCAATGCGA
1 A-TCGCAATGCGA
377152 TTTGTGTTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 8 0.22
16 4 0.11
17 4 0.11
18 3 0.08
19 17 0.47
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:377182 original size:14 final size:14
Alignment explanation
Indices: 377163--377252 Score: 81
Period size: 14 Copynumber: 5.8 Consensus size: 14
377153 TTGTGTTTCG
377163 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
377177 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
377193 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
377209 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
377226 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
377242 CGTTGCGATTT
1 CGTTGCGATTT
377253 GCATTTCGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 26 0.41
15 3 0.05
16 12 0.19
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:377227 original size:33 final size:33
Alignment explanation
Indices: 377158--377269 Score: 199
Period size: 33 Copynumber: 3.4 Consensus size: 33
377148 GCGATTTGTG
*
377158 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
377190 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
377223 TTTCGCATTGCGATTTTGTCGTTGCGATTTGCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
377256 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
377270 AGCCATTTCC
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:377288 original size:20 final size:19
Alignment explanation
Indices: 377254--377309 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
377244 TTGCGATTTG
*
377254 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
377273 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
377293 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
377310 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:379148 original size:14 final size:14
Alignment explanation
Indices: 379114--379152 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
379104 TTGATTGTTT
379114 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
379128 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
379142 TGTTGATTTGT
1 AATTGATTTGT
379153 TTTAATTGGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:379312 original size:19 final size:19
Alignment explanation
Indices: 379288--379355 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
379278 ATCGCAACGA
379288 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
**
379307 GAAAATCGCAATATGAAAT
1 GAAAATCGCAATGCGAAAT
379326 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
379340 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
379356 TTTTCATTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 1 0.02
19 28 0.65
ACGTcount: A:0.49, C:0.16, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:379373 original size:19 final size:19
Alignment explanation
Indices: 379345--379398 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
379335 AACGAGAAAA
*
379345 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
379364 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
379383 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
379399 TAGTTGTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:379451 original size:40 final size:39
Alignment explanation
Indices: 379345--379470 Score: 129
Period size: 40 Copynumber: 3.4 Consensus size: 39
379335 AACGAGAAAA
* * ***
379345 TCGCAATGCGATTTTCATTTCGCATTGCGATTTTCA-TT
1 TCGCATTGCGATTTTCATTTCGAATTGCGATAGCCATTT
* *
379383 TCGCATTGCGATTTTC---T--AGTTGTGATAGCCATTT
1 TCGCATTGCGATTTTCATTTCGAATTGCGATAGCCATTT
379417 TCGCATTGCGATTTTTCATTTCGAATTGCGATAGCCATTT
1 TCGCATTGCGA-TTTTCATTTCGAATTGCGATAGCCATTT
*
379457 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
379471 CCCCTTGCGA
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
33 8 0.11
34 13 0.18
35 6 0.08
38 16 0.23
39 3 0.04
40 25 0.35
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (39 bp):
TCGCATTGCGATTTTCATTTCGAATTGCGATAGCCATTT
Found at i:379465 original size:20 final size:20
Alignment explanation
Indices: 379406--379468 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
379396 TTCTAGTTGT
379406 GATAGCCATTTTCGCATTGC
1 GATAGCCATTTTCGCATTGC
*** *
379426 GATTTTTCA-TTTCGAATTGC
1 GA-TAGCCATTTTCGCATTGC
*
379446 GATAGCCATTTTCGCGTTGC
1 GATAGCCATTTTCGCATTGC
379466 GAT
1 GAT
379469 TTCCCCTTGC
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
19 3 0.09
20 26 0.81
21 3 0.09
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
GATAGCCATTTTCGCATTGC
Found at i:379704 original size:20 final size:20
Alignment explanation
Indices: 379679--379790 Score: 73
Period size: 20 Copynumber: 5.5 Consensus size: 20
379669 TTTGAAGATG
379679 ATTGCGATTTTCAGAATCTC
1 ATTGCGATTTTCAGAATCTC
***
379699 ATTGCGAAAGTCAGAATCTC
1 ATTGCGATTTTCAGAATCTC
* * **
379719 GTTGCGATTTTGTATTATCTC
1 ATTGCGATTTT-CAGAATCTC
* ** * *
379740 GTTGCGATAGTCAGTATCAC
1 ATTGCGATTTTCAGAATCTC
*
379760 ATTGCGATTTTCCA-AATTCGC
1 ATTGCGATTTT-CAGAA-TCTC
379781 ATTGCGATTT
1 ATTGCGATTT
379791 ACTTATTCGC
Statistics
Matches: 69, Mismatches: 20, Indels: 5
0.73 0.21 0.05
Matches are distributed among these distances:
20 39 0.57
21 30 0.43
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTGCGATTTTCAGAATCTC
Found at i:379785 original size:21 final size:20
Alignment explanation
Indices: 379759--379821 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
379749 GTCAGTATCA
*
379759 CATTGCGATTTTCCAAATTCG
1 CATTGCGA-TTTACAAATTCG
**
379780 CATTGCGATTTACTTATTCG
1 CATTGCGATTTACAAATTCG
* * *
379800 CATTGCGAATTAGAAAATCG
1 CATTGCGATTTACAAATTCG
379820 CA
1 CA
379822 ACGCGATACT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (20 bp):
CATTGCGATTTACAAATTCG
Found at i:380605 original size:24 final size:24
Alignment explanation
Indices: 380578--380624 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
380568 GTATTCGAAA
*
380578 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
*
380602 TTTGATATTGGTCAATACTCGGA
1 TTTGATATTGGTCAATACCCGGA
380625 TTTTAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:383123 original size:19 final size:19
Alignment explanation
Indices: 383101--383184 Score: 115
Period size: 19 Copynumber: 4.7 Consensus size: 19
383091 GGAAATTACT
383101 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
383120 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
383134 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
383153 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
383172 ATCGCAACGCGAA
1 ATCGCAATGCGAA
383185 TTTAATTTCG
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:383202 original size:19 final size:19
Alignment explanation
Indices: 383180--383254 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
383170 AAATCGCAAC
*
383180 GCGAATTTAATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
383199 GCG-A-TTC---TCTCGTT
1 GCGAATTTCATTTCGCGTT
*
383213 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
383232 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
383251 GCGA
1 GCGA
383255 TAGTACTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 9 0.20
16 3 0.07
17 2 0.04
18 1 0.02
19 31 0.67
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:383255 original size:19 final size:19
Alignment explanation
Indices: 383211--383255 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
383201 GATTCTCTCG
*
383211 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
383230 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
383249 TTGCGAT
1 TTGCGAT
383256 AGTACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:383382 original size:14 final size:14
Alignment explanation
Indices: 383363--383399 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
383353 CATCAATTAA
383363 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
383377 ACAAATCACCTTTT
1 ACAAATCAACTTTT
383391 ACAAATCAA
1 ACAAATCAA
383400 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:385264 original size:91 final size:90
Alignment explanation
Indices: 385090--385274 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
385080 ATTTCAAACT
*
385090 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
385155 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
385183 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACATTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
385247 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
385274 T
1 T
385275 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:387024 original size:14 final size:14
Alignment explanation
Indices: 387005--387060 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
386995 GGAAATGACT
387005 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
387019 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
387036 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
387052 ATCGCAACG
1 ATCGCAACG
387061 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:387038 original size:33 final size:33
Alignment explanation
Indices: 386981--387079 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
386971 ACGAGATAAT
386981 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
387015 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
387048 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
387080 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 49 0.78
34 14 0.22
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:387043 original size:19 final size:18
Alignment explanation
Indices: 386956--387134 Score: 130
Period size: 19 Copynumber: 10.1 Consensus size: 18
386946 TCTTTTGGTT
*
386956 GAAATGAAAATCGCAACGA
1 GAAATG-AAATCGCAACGC
386975 GATAATGAGAATCGCAACGC
1 GA-AATGA-AATCGCAACGC
*
386995 GGAAATGACTATCGCAA--C
1 -GAAATGA-AATCGCAACGC
*
387013 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
*
387029 GAAATGACTATCGCAA--C
1 GAAATGA-AATCGCAACGC
*
387046 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
387062 GAAATGAAAATCGCAACGC
1 GAAATG-AAATCGCAACGC
387081 GAAATGAAAATCGCAA--C
1 GAAATG-AAATCGCAACGC
*
387098 GAGA-G-AATCGCAACGC
1 GAAATGAAATCGCAACGC
*
387114 GAAATGAAAATCGCAATGC
1 GAAATG-AAATCGCAACGC
387133 GA
1 GA
387135 TTTTGGTTTC
Statistics
Matches: 129, Mismatches: 13, Indels: 36
0.72 0.07 0.20
Matches are distributed among these distances:
14 22 0.17
16 15 0.12
17 14 0.11
18 1 0.01
19 49 0.38
20 26 0.20
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.12
Consensus pattern (18 bp):
GAAATGAAATCGCAACGC
Found at i:387083 original size:52 final size:52
Alignment explanation
Indices: 387018--387134 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
387008 GCAACGAGAG
**
387018 AATCGCAACGCGAAATGACTATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
387070 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
*
387122 AATCGCAATGCGA
1 AATCGCAACGCGA
387135 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
Found at i:387163 original size:19 final size:19
Alignment explanation
Indices: 387130--387174 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
387120 AAAATCGCAA
*
387130 TGCGATTTTGGTTTCGCGC
1 TGCGATTTTGATTTCGCGC
* *
387149 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGC
387168 TGCGATT
1 TGCGATT
387175 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGC
Found at i:387770 original size:20 final size:20
Alignment explanation
Indices: 387729--387800 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
387719 GCTATGTAAA
* *
387729 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-TTACGTAT
387749 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* * *
387769 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTACGT-AT
387790 TCGCATTGCGA
1 TCGCATTGCGA
387801 ATTATGAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.07
20 29 0.66
21 12 0.27
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:387814 original size:21 final size:21
Alignment explanation
Indices: 387790--387862 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
387780 TTTTCCTAAT
*
387790 TCGCATTGCGAATTATGAAAA
1 TCGCAATGCGAATTATGAAAA
* * *
387811 TCGCAACGCGAA-TACGTAAA
1 TCGCAATGCGAATTATGAAAA
387831 TCGCAATGCGAATT-TGGAAAA
1 TCGCAATGCGAATTAT-GAAAA
* *
387852 TTGCATTGCGA
1 TCGCAATGCGA
387863 TAGTCAGTAT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAATTATGAAAA
Found at i:387994 original size:21 final size:21
Alignment explanation
Indices: 387954--387994 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
387944 ACTGTAGACC
** *
387954 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
387975 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
387995 GTGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:395337 original size:60 final size:60
Alignment explanation
Indices: 395252--395399 Score: 183
Period size: 60 Copynumber: 2.5 Consensus size: 60
395242 GATTCTTATC
* * * * *
395252 TAAATTGGT-CTCTAAACTTTTGAACATTTTAATTTCATTCTTAAACTAT-AACTCTTATTA
1 TAAATTGGTCCCCT-AACTTTTGAACATTTCAAATTCATCCTCAAACTATGAAC-CTTATTA
*
395312 TAAATTGGTCCCCTAACTTTTGAACATTTCAAATTCATCCTCAAACTATGAACCTTATTC
1 TAAATTGGTCCCCTAACTTTTGAACATTTCAAATTCATCCTCAAACTATGAACCTTATTA
* * *
395372 TAAGTTAGTCCCCAAACTTTTGAACATT
1 TAAATTGGTCCCCTAACTTTTGAACATT
395400 CCAATGATAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
60 71 0.92
61 6 0.08
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (60 bp):
TAAATTGGTCCCCTAACTTTTGAACATTTCAAATTCATCCTCAAACTATGAACCTTATTA
Found at i:402689 original size:20 final size:20
Alignment explanation
Indices: 402664--402754 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
402654 TAAATTAAAT
*
402664 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
402684 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
402704 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
402716 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
402736 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
402755 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:402779 original size:53 final size:52
Alignment explanation
Indices: 402663--402812 Score: 275
Period size: 53 Copynumber: 2.9 Consensus size: 52
402653 CTAAATTAAA
*
402663 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
402715 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
402768 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
402813 GTTGCTAATT
Statistics
Matches: 96, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 10 0.10
52 35 0.36
53 51 0.53
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:402794 original size:20 final size:20
Alignment explanation
Indices: 402769--402808 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
402759 TCTATTAGTT
*
402769 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
402789 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
402809 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:406840 original size:20 final size:20
Alignment explanation
Indices: 406815--406861 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
406805 TGGAGGAGCA
406815 AGAAGCAACCAGTTGTCTCT
1 AGAAGCAACCAGTTGTCTCT
406835 AGAAGCAACCAGTTGTCTCT
1 AGAAGCAACCAGTTGTCTCT
406855 AGAAGCA
1 AGAAGCA
406862 GTGCGGAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
AGAAGCAACCAGTTGTCTCT
Found at i:407295 original size:20 final size:21
Alignment explanation
Indices: 407270--407309 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
407260 TCTATTAGTT
*
407270 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
407290 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTT
407310 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:407324 original size:53 final size:52
Alignment explanation
Indices: 407238--407366 Score: 233
Period size: 53 Copynumber: 2.5 Consensus size: 52
407228 TAAATTAAAT
*
407238 ATTAGATAGGATCAGTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
407290 ATTAGATAGAATCAGTTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAG-TTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
407343 ATTAGATAGAATCA-TTTTTATTCT
1 ATTAGATAGAATCAGTTTTTATTCT
407367 GTTGCTAATT
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 10 0.13
52 14 0.19
53 51 0.68
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (52 bp):
ATTAGATAGAATCAGTTTTTATTCTATTAGTTATTAGATAGGATCATTTTTA
Found at i:407348 original size:20 final size:20
Alignment explanation
Indices: 407323--407362 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
407313 TCTATTAGTT
*
407323 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
407343 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
407363 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:418047 original size:45 final size:45
Alignment explanation
Indices: 417998--418086 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
417988 GAGTCATTCA
* *
417998 CTGTCACAGG-CATCTCTTTGTTCATCCTCTCAGCTGAACTATTTG
1 CTGTCA-AGGCCATCACTTTCTTCATCCTCTCAGCTGAACTATTTG
* * *
418043 CTGTCAAGGCCATCACTTTCTTCATCTTCTCAGGTGAGCTATTT
1 CTGTCAAGGCCATCACTTTCTTCATCCTCTCAGCTGAACTATTT
418087 ACTGCCATCG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
44 3 0.08
45 35 0.92
ACGTcount: A:0.18, C:0.28, G:0.16, T:0.38
Consensus pattern (45 bp):
CTGTCAAGGCCATCACTTTCTTCATCCTCTCAGCTGAACTATTTG
Found at i:418229 original size:39 final size:42
Alignment explanation
Indices: 418058--418216 Score: 132
Period size: 42 Copynumber: 3.8 Consensus size: 42
418048 AAGGCCATCA
*
418058 CTTTCTTCATCTTCTCAGGTGAGCTATTTACTGCCATCGTC-C-
1 CTTTC-TCATCTTCTCAGCTGAGCTATTTACTGCCATCG-CACT
* *
418100 CTTGACTCATCTTCTCAGCTGAGCTATTTACTGCCATGGCCAACT
1 CTT-TCTCATCTTCTCAGCTGAGCTATTTACTGCCATCG-C-ACT
* * * * * *
418145 CTTTCTTCCTCTTCTCAGATGAACTATTCACAG-C-T-G-TCT
1 CTTTC-TCATCTTCTCAGCTGAGCTATTTACTGCCATCGCACT
418184 CTTTCTCAATCTTCTCAGCTGAGCTATTTACTG
1 CTTTCTC-ATCTTCTCAGCTGAGCTATTTACTG
418217 TCATGACCTT
Statistics
Matches: 95, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
38 2 0.02
39 27 0.28
42 36 0.38
43 2 0.02
44 3 0.03
45 25 0.26
ACGTcount: A:0.18, C:0.30, G:0.13, T:0.39
Consensus pattern (42 bp):
CTTTCTCATCTTCTCAGCTGAGCTATTTACTGCCATCGCACT
Found at i:418231 original size:84 final size:87
Alignment explanation
Indices: 418019--418256 Score: 261
Period size: 84 Copynumber: 2.8 Consensus size: 87
418009 ATCTCTTTGT
* * * * * * *
418019 TCATCCTCTCAGCTGAACTATTTGCTGTCAAGGCCATCACTTTCTTCATCTTCTCAGGTGAGCTA
1 TCATCTTCTCAGCTGAGCTATTTACTGTCATGGCCATCTCTTTCTTCATCTTCTCAGATGAACTA
* *
418084 TTTACTGCCATCGTCCCTTGAC
66 TTCACAGCCATCGTCCCTTGAC
* * *
418106 TCATCTTCTCAGCTGAGCTATTTACTGCCATGGCCAACTCTTTCTTCCTCTTCTCAGATGAACTA
1 TCATCTTCTCAGCTGAGCTATTTACTGTCATGGCCATCTCTTTCTTCATCTTCTCAGATGAACTA
* *
418171 TTCACAG-C-T-GTCTCTT-TC
66 TTCACAGCCATCGTCCCTTGAC
* * * *
418189 TCAATCTTCTCAGCTGAGCTATTTACTGTCATGACCTTCTCTTTCTTCAT-TTCATCAGCTGAAT
1 TC-ATCTTCTCAGCTGAGCTATTTACTGTCATGGCCATCTCTTTCTTCATCTTC-TCAGATGAAC
418253 TATT
64 TATT
418257 TGTTGTCATG
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
83 6 0.05
84 60 0.47
85 1 0.01
86 1 0.01
87 60 0.47
ACGTcount: A:0.19, C:0.29, G:0.13, T:0.39
Consensus pattern (87 bp):
TCATCTTCTCAGCTGAGCTATTTACTGTCATGGCCATCTCTTTCTTCATCTTCTCAGATGAACTA
TTCACAGCCATCGTCCCTTGAC
Found at i:418232 original size:45 final size:44
Alignment explanation
Indices: 418010--418250 Score: 187
Period size: 45 Copynumber: 5.6 Consensus size: 44
418000 GTCACAGGCA
* * * * * *
418010 TCTCTTTGTTCATCCTCTCAGCTGAACTATTTGCTGTCAAGGCC
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGCCATGGCC
* * *
418054 ATCACTTTCTTCATCTTCTCAGGTGAGCTATTTACTGCCATCGTCC
1 -TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGCCAT-GGCC
**
418100 -CT-TGAC-TCATCTTCTCAGCTGAGCTATTTACTGCCATGGCC
1 TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGCCATGGCC
* * * * * *
418141 AACTCTTTCTTCCTCTTCTCAGATGAACTATTCACAG-C-T-G--
1 -TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGCCATGGCC
* *
418181 TCTCTTTC-TCAATCTTCTCAGCTGAGCTATTTACTGTCATGACC
1 TCTCTTTCTTC-ATCTTCTCAGCTGAGCTATTTACTGCCATGGCC
418225 TTCTCTTTCTTCAT-TTCATCAGCTGA
1 -TCTCTTTCTTCATCTTC-TCAGCTGA
418251 ATTATTTGTT
Statistics
Matches: 154, Mismatches: 28, Indels: 28
0.73 0.13 0.13
Matches are distributed among these distances:
38 2 0.01
39 27 0.18
40 1 0.01
41 4 0.03
42 31 0.20
43 5 0.03
44 7 0.05
45 72 0.47
46 5 0.03
ACGTcount: A:0.18, C:0.30, G:0.13, T:0.39
Consensus pattern (44 bp):
TCTCTTTCTTCATCTTCTCAGCTGAGCTATTTACTGCCATGGCC
Found at i:418275 original size:45 final size:46
Alignment explanation
Indices: 418176--418277 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 46
418166 AACTATTCAC
*
418176 AGCTGTCTCTTTCTCAATCTTCTCAGCTGAGCTATTTACTGTCATG
1 AGCTGTCTCTTTCTCAATCTTCTCAGCTGAACTATTTACTGTCATG
* * **
418222 ACCT-TCTCTTTCTTC-AT-TTCATCAGCTGAATTATTTGTTGTCATG
1 AGCTGTCTCTTTC-TCAATCTTC-TCAGCTGAACTATTTACTGTCATG
418267 -GCTGTCTCTTT
1 AGCTGTCTCTTT
418278 GTTTGTCTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
44 5 0.11
45 37 0.79
46 5 0.11
ACGTcount: A:0.16, C:0.25, G:0.14, T:0.46
Consensus pattern (46 bp):
AGCTGTCTCTTTCTCAATCTTCTCAGCTGAACTATTTACTGTCATG
Found at i:423832 original size:21 final size:21
Alignment explanation
Indices: 423803--423867 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 21
423793 ATCTATAAAA
*
423803 TAAAA-TATTATATTATATTT
1 TAAAATTATTATAATATATTT
423823 TAAAATTATTAATAAATATATTT
1 TAAAATTATT-AT-AATATATTT
*
423846 TAAGGAATTTTTATAATATATT
1 TAA--AATTATTATAATATATT
423868 AGACTACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 5 0.13
21 4 0.11
22 2 0.05
23 19 0.50
24 2 0.05
25 6 0.16
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TAAAATTATTATAATATATTT
Found at i:424039 original size:26 final size:26
Alignment explanation
Indices: 423988--424049 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
423978 TATTATTAAA
*
423988 ATAAGAATATAATAGTATTATATATT
1 ATAATAATATAATAGTATTATATATT
*
424014 ATTATAATATAATTGAGTA-TAT-TATT
1 ATAATAATATAA-T-AGTATTATATATT
424040 ATAATAATAT
1 ATAATAATAT
424050 TATTATGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 23 0.74
27 4 0.13
28 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (26 bp):
ATAATAATATAATAGTATTATATATT
Done.