Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000575.1 Hibiscus syriacus cultivar Beakdansim tig00001127_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: 111029
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:5501 original size:2 final size:2
Alignment explanation
Indices: 5494--5523 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5484 TAATAAATTC
5494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5524 TTTGTTCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10916 original size:29 final size:29
Alignment explanation
Indices: 10870--10954 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
10860 TAGTTTTCTG
* *
10870 GAAA-TTGAATTTTAAAAAATGAATTACT
1 GAAATTTGAATTATGAAAAATGAATTACT
10898 GAAATTTGAATTATGAAAAATGAATTACT
1 GAAATTTGAATTATGAAAAATGAATTACT
* *
10927 GAAATTTGAATTCTGGAAAATGAATTAC
1 GAAATTTGAATTATGAAAAATGAATTAC
10955 ATTTATGGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 4 0.08
29 48 0.92
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (29 bp):
GAAATTTGAATTATGAAAAATGAATTACT
Found at i:10921 original size:14 final size:15
Alignment explanation
Indices: 10884--10954 Score: 83
Period size: 14 Copynumber: 4.9 Consensus size: 15
10874 TTGAATTTTA
10884 AAAAATGAATTACTG
1 AAAAATGAATTACTG
**
10899 AAATTTGAATTA-TG
1 AAAAATGAATTACTG
10913 AAAAATGAATTACTG
1 AAAAATGAATTACTG
**
10928 AAATTTGAATT-CTG
1 AAAAATGAATTACTG
*
10942 GAAAATGAATTAC
1 AAAAATGAATTAC
10955 ATTTATGGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
14 23 0.51
15 22 0.49
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (15 bp):
AAAAATGAATTACTG
Found at i:10945 original size:15 final size:15
Alignment explanation
Indices: 10889--10938 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
10879 TTTTAAAAAA
10889 TGAATTACTGAAATT
1 TGAATTACTGAAATT
**
10904 TGAATTA-TGAAAAA
1 TGAATTACTGAAATT
10918 TGAATTACTGAAATT
1 TGAATTACTGAAATT
10933 TGAATT
1 TGAATT
10939 CTGGAAAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.38
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:10981 original size:34 final size:34
Alignment explanation
Indices: 10943--11026 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
10933 TGAATTCTGG
10943 AAAATGAATTACATTTATGGAAAACGTTTTCCGT
1 AAAATGAATTACATTTATGGAAAACGTTTTCCGT
10977 AAAATGAATTACATTTATGGAAAACGTTTTCCGT
1 AAAATGAATTACATTTATGGAAAACGTTTTCCGT
*
11011 AGAATGAATTACATTT
1 AAAATGAATTACATTT
11027 TTCTGGAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (34 bp):
AAAATGAATTACATTTATGGAAAACGTTTTCCGT
Found at i:11386 original size:30 final size:30
Alignment explanation
Indices: 11312--11416 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 30
11302 AGTAATAGTG
* *
11312 TTATATTTATTTTAAAAATATTAATTATATT-
1 TTATATTAATATT-AAAATATT-ATTATATTA
*** *
11343 TTATATCCTTATTAAAATATTATTAGATTA
1 TTATATTAATATTAAAATATTATTATATTA
* *
11373 TTATATTAATATTAAATATATAATAATATTA
1 TTATATTAATATTAAA-ATATTATTATATTA
11404 TTCATTATTAATA
1 TT-A-TATTAATA
11417 ATTTAATAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 7 0.12
30 21 0.36
31 22 0.37
32 1 0.02
33 8 0.14
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (30 bp):
TTATATTAATATTAAAATATTATTATATTA
Found at i:11417 original size:19 final size:19
Alignment explanation
Indices: 11351--11418 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
11341 TTTTATATCC
11351 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
* *
11370 TTATT-ATATTAATATTAA
1 TTATTAATAATATTATTAA
* *
11388 ATATATAATAATATTATTCA
1 TTAT-TAATAATATTATTAA
11408 TTATTAATAAT
1 TTATTAATAAT
11419 TTAATAATAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
18 5 0.13
19 21 0.54
20 13 0.33
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:11544 original size:11 final size:11
Alignment explanation
Indices: 11528--11612 Score: 51
Period size: 11 Copynumber: 8.2 Consensus size: 11
11518 ATTGATTACT
*
11528 TTATTATAATA
1 TTATTAAAATA
11539 TTATTAAAATA
1 TTATTAAAATA
*
11550 TTAATAAATATA
1 TTATTAAA-ATA
11562 TT-TT-AAATA
1 TTATTAAAATA
11571 TT-TT--AATA
1 TTATTAAAATA
* *
11579 --ATTAATATT
1 TTATTAAAATA
11588 TTGATTAAAATGA
1 TT-ATTAAAAT-A
11601 -TATTAAAATA
1 TTATTAAAATA
11611 TT
1 TT
11613 TTATTAATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
7 2 0.03
8 4 0.07
9 9 0.16
10 3 0.05
11 27 0.47
12 13 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
TTATTAAAATA
Found at i:11576 original size:23 final size:23
Alignment explanation
Indices: 11533--11589 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
11523 TTACTTTATT
11533 ATAATATTATTAAAATATTAATAA
1 ATAATATT-TTAAAATATTAATAA
*
11557 AT-ATATTTTAAATATTTTAATAA
1 ATAATATTTTAAA-ATATTAATAA
*
11580 TTAATATTTT
1 ATAATATTTT
11590 GATTAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.17
23 15 0.52
24 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATAATATTTTAAAATATTAATAA
Found at i:12323 original size:24 final size:25
Alignment explanation
Indices: 12290--12338 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
12280 TTTTATTTTA
*
12290 TTAATTTAATATTAAT-AAAATATT
1 TTAATATAATATTAATCAAAATATT
*
12314 TTAATATAATTTTAATCAAAATATT
1 TTAATATAATATTAATCAAAATATT
12339 AATTATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAATATAATATTAATCAAAATATT
Found at i:12403 original size:21 final size:21
Alignment explanation
Indices: 12379--12437 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
12369 AATATTTCTA
12379 ATAAATAATATATATAATATT
1 ATAAATAATATATATAATATT
*
12400 AT-AATAAAATA-ATAA-ATT
1 ATAAATAATATATATAATATT
12418 ATATTAATAATATAT-TAATA
1 ATA--AATAATATATATAATA
12438 ATAATAAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 4 0.13
20 8 0.26
21 13 0.42
22 1 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAATAATATATATAATATT
Found at i:12413 original size:32 final size:31
Alignment explanation
Indices: 12377--12455 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 31
12367 TTAATATTTC
*
12377 TAATAAATAATATATATAATATTATAATAA-AA
1 TAATAAAT-ATATAT-TAATAATATAATAATAA
*
12409 TAATAAAT-TATATTAATAATATATTAATAA
1 TAATAAATATATATTAATAATATAATAATAA
12439 TAATAAGATATTATATT
1 TAATAA-ATA-TATATT
12456 TTTTTTTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 12 0.29
30 13 0.32
31 2 0.05
32 8 0.20
33 6 0.15
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (31 bp):
TAATAAATATATATTAATAATATAATAATAA
Found at i:12427 original size:24 final size:24
Alignment explanation
Indices: 12368--12453 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 24
12358 ATATATTTAT
*
12368 TAATATTTCTAAT-AAATAATATATA
1 TAATA-TTATAATAAAATAATA-ATA
12393 TAATATTATAATAAAATAATAA-A
1 TAATATTATAATAAAATAATAATA
*
12416 TTATATTAATAATATATTAATAATAATA
1 TAATATT-ATAATA-A--AATAATAATA
12444 -AGATATTATA
1 TA-ATATTATA
12454 TTTTTTTTTA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
23 7 0.14
24 13 0.25
25 14 0.27
27 11 0.22
28 6 0.12
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (24 bp):
TAATATTATAATAAAATAATAATA
Found at i:12431 original size:11 final size:11
Alignment explanation
Indices: 12338--12440 Score: 58
Period size: 11 Copynumber: 9.5 Consensus size: 11
12328 ATCAAAATAT
12338 TAAT-TATTAA
1 TAATATATTAA
12348 -AATAT-TTAA
1 TAATATATTAA
*
12357 -AATATATTTAT
1 TAATATA-TTAA
*
12368 TAATATTTCTAA
1 TAATATAT-TAA
12380 TAA-ATAATATATA
1 TAATAT-AT-TA-A
12393 TAATAT-TATAA
1 TAATATAT-TAA
* *
12404 TAAAATAATAA
1 TAATATATTAA
*
12415 -ATTATATTAA
1 TAATATATTAA
12425 TAATATATTAA
1 TAATATATTAA
12436 TAATA
1 TAATA
12441 ATAAGATATT
Statistics
Matches: 72, Mismatches: 11, Indels: 19
0.71 0.11 0.19
Matches are distributed among these distances:
9 12 0.17
10 8 0.11
11 29 0.40
12 17 0.24
13 4 0.06
14 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (11 bp):
TAATATATTAA
Found at i:12497 original size:42 final size:40
Alignment explanation
Indices: 12382--12507 Score: 107
Period size: 41 Copynumber: 3.1 Consensus size: 40
12372 ATTTCTAATA
*
12382 AATAATATATATAATATTATAATAAAATAA-TAAATTA--TATT
1 AATAATATAT-TAATA--ATAATAAAA-AATTATATTATTTATT
* * * *
12423 AATAATATATTAATAATAATAAGATATTATATTTTTTTTT
1 AATAATATATTAATAATAATAAAAAATTATATTATTTATT
*
12463 AATAATATA-TAATAAGTTATTAAAAAATGTATATTATTTATT
1 AATAATATATTAATAA--TAATAAAAAAT-TATATTATTTATT
12505 AAT
1 AAT
12508 TTAATAGAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
37 1 0.01
38 13 0.19
39 6 0.09
40 17 0.25
41 18 0.26
42 14 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (40 bp):
AATAATATATTAATAATAATAAAAAATTATATTATTTATT
Found at i:12583 original size:21 final size:19
Alignment explanation
Indices: 12546--12585 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
12536 TATATTAATA
12546 TAATAATCTAA-TAATATT
1 TAATAATCTAATTAATATT
12564 TAATATATACTAATTAATATT
1 TAATA-AT-CTAATTAATATT
12585 T
1 T
12586 TTAAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 2 0.11
20 4 0.21
21 8 0.42
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATAATCTAATTAATATT
Found at i:12588 original size:23 final size:24
Alignment explanation
Indices: 12540--12595 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
12530 TATATTTATA
12540 TTAATATA-ATAATCTAATAATAT
1 TTAATATATATAATCTAATAATAT
*
12563 TTAATATATACTAAT-TAAT-ATTT
1 TTAATATATA-TAATCTAATAATAT
*
12586 TTAAAATATA
1 TTAATATATA
12596 ATATAACACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 20 0.69
24 5 0.17
25 4 0.14
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAATATATATAATCTAATAATAT
Found at i:12783 original size:22 final size:23
Alignment explanation
Indices: 12725--12785 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
12715 AATTATTTTA
*
12725 ATATTTTA-AAAATAATAATATT
1 ATATTTTATTAAATAATAATATT
* *
12747 AAATTTTATGATAAATAATATTATT
1 ATATTTTAT--TAAATAATAATATT
12772 -TATTTTATTAAATA
1 ATATTTTATTAAATA
12786 TTTATAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 13 0.41
24 7 0.22
25 12 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTTTATTAAATAATAATATT
Found at i:21463 original size:15 final size:15
Alignment explanation
Indices: 21439--21477 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
21429 AAGTTATAAA
21439 ATTTTGAAATATTAT
1 ATTTTGAAATATTAT
*
21454 ATTTT-CAA-ATTAT
1 ATTTTGAAATATTAT
21467 ATTTTGAAATA
1 ATTTTGAAATA
21478 CAATCTGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
13 10 0.50
14 4 0.20
15 6 0.30
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
ATTTTGAAATATTAT
Found at i:26026 original size:41 final size:41
Alignment explanation
Indices: 25981--26224 Score: 434
Period size: 41 Copynumber: 5.9 Consensus size: 41
25971 ACGCGATAGT
*
25981 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
*
26022 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACATG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
*
26063 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGA
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
26104 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
26145 CGAAGTTCGCATTGCGATTCATTCCAAATTCGTTGCGACAGG
1 CGAAGTTCGCATTGCGATTCATTCC-AATTCGTTGCGACAGG
*
26187 CGAAGTTCGCGTTGCGATTCATTCCAAATTCGTTGCGA
1 CGAAGTTCGCATTGCGATTCATTCC-AATTCGTTGCGA
26225 TAGTCCAAAT
Statistics
Matches: 196, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
41 143 0.73
42 53 0.27
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (41 bp):
CGAAGTTCGCATTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:26233 original size:19 final size:19
Alignment explanation
Indices: 26167--26234 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 19
26157 TGCGATTCAT
*
26167 TCCAAATTCGTTGCGACAG
1 TCCAAATTCGTTGCGATAG
* * * *
26186 GCGAAGTTCGCGTTGCGATTCAT
1 TCCAAATT--CGTTGCGA-T-AG
26209 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
26228 TCCAAAT
1 TCCAAAT
26235 ATTGCATTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
19 13 0.36
20 1 0.03
21 16 0.44
23 6 0.17
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:27105 original size:19 final size:19
Alignment explanation
Indices: 27081--27148 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
27071 CAAATGCAAT
27081 ATTTGGACTATCGCAACGA
1 ATTTGGACTATCGCAACGA
*
27100 ATTTGGAATGAATCGCAACGCGA
1 ATTTGGACT--ATCGCAA--CGA
* * *
27123 ACTTCGCCTATCGCAACGA
1 ATTTGGACTATCGCAACGA
27142 ATTTGGA
1 ATTTGGA
27149 ATGAATCGCA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 15 0.41
21 14 0.38
23 8 0.22
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (19 bp):
ATTTGGACTATCGCAACGA
Found at i:27147 original size:42 final size:42
Alignment explanation
Indices: 27088--27384 Score: 494
Period size: 41 Copynumber: 7.2 Consensus size: 42
27078 AATATTTGGA
27088 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
27130 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
27172 CTGTCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* *
27213 ATGTCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* *
27254 CTGTCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
27295 CTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* * *
27336 CTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
27378 CTATCGC
1 CTATCGC
27385 GTTGCGAATC
Statistics
Matches: 244, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
40 1 0.00
41 155 0.64
42 88 0.36
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:31685 original size:18 final size:18
Alignment explanation
Indices: 31664--31708 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
31654 ATAGTTGTCA
31664 TTCGGGACACAATGGTCC
1 TTCGGGACACAATGGTCC
* *
31682 TTCGGGACATAGTGGTCC
1 TTCGGGACACAATGGTCC
*
31700 TACGGGACA
1 TTCGGGACA
31709 AATTTCTATG
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:0.22, C:0.24, G:0.31, T:0.22
Consensus pattern (18 bp):
TTCGGGACACAATGGTCC
Found at i:31690 original size:36 final size:36
Alignment explanation
Indices: 31640--31708 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
31630 GGATTATCAG
* * *
31640 TGGTCTTTCAGGACATAGTTGTCATTCGGGACACAA
1 TGGTCCTTCAGGACATAGTGGTCATACGGGACACAA
* *
31676 TGGTCCTTCGGGACATAGTGGTCCTACGGGACA
1 TGGTCCTTCAGGACATAGTGGTCATACGGGACA
31709 AATTTCTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (36 bp):
TGGTCCTTCAGGACATAGTGGTCATACGGGACACAA
Found at i:35243 original size:21 final size:21
Alignment explanation
Indices: 35217--35258 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
35207 AGTTTATTTT
35217 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
35238 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
35259 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:35295 original size:33 final size:33
Alignment explanation
Indices: 35253--35351 Score: 173
Period size: 33 Copynumber: 3.0 Consensus size: 33
35243 TTTGTTTCAA
35253 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
35286 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
35319 TTATCGAACTTGGAAGTATTT-AGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
35351 T
1 T
35352 ATTGTAAACT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 11 0.17
33 53 0.83
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:36121 original size:2 final size:2
Alignment explanation
Indices: 36114--36167 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
36104 TGTAAGAAAG
36114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36156 AT AT AT AT AT AT
1 AT AT AT AT AT AT
36168 TGAGTATCGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36676 original size:10 final size:10
Alignment explanation
Indices: 36646--36679 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
36636 TATTTGGGTG
36646 TTATATAAGC
1 TTATATAAGC
*
36656 TTAAATAAAGC
1 TTATAT-AAGC
36667 TTATATAAGC
1 TTATATAAGC
36677 TTA
1 TTA
36680 AAACACCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (10 bp):
TTATATAAGC
Found at i:38123 original size:18 final size:18
Alignment explanation
Indices: 38018--38115 Score: 142
Period size: 18 Copynumber: 5.4 Consensus size: 18
38008 GGGATTATTT
* *
38018 GTGGTCTTTCGTGACATA
1 GTGGTCCTTCGGGACATA
* *
38036 GTGGTCATTCGGGACACA
1 GTGGTCCTTCGGGACATA
*
38054 GTGGTCCTTCGGGACACA
1 GTGGTCCTTCGGGACATA
*
38072 ATGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
38090 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
38108 GTGGTCCT
1 GTGGTCCT
38116 ACGAGACAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 73 1.00
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:39003 original size:4 final size:4
Alignment explanation
Indices: 38988--39328 Score: 622
Period size: 4 Copynumber: 86.5 Consensus size: 4
38978 CATGTAACAA
*
38988 ATAC ACTAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC A-TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39037 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39085 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39133 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39181 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT-- ATAC ATAC AT-- ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39225 ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39271 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
39319 ATAC ATAC AT
1 ATAC ATAC AT
39329 GTCATTATCA
Statistics
Matches: 328, Mismatches: 2, Indels: 14
0.95 0.01 0.04
Matches are distributed among these distances:
2 6 0.02
4 318 0.97
5 4 0.01
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:39720 original size:18 final size:18
Alignment explanation
Indices: 39694--39766 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
39684 ACTGAATATT
* * *
39694 TGTCTCGAATAACCAATA
1 TGTCCCGAAGAACCACTA
*
39712 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGAACCACT-A
*
39731 CTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGAACCACTA
*
39750 TGTCCCGAAGGACCACT
1 TGTCCCGAAGAACCACT
39767 GTTTGTCTCG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 28 0.62
19 2 0.04
20 15 0.33
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGAACCACTA
Found at i:39741 original size:20 final size:19
Alignment explanation
Indices: 39711--39789 Score: 81
Period size: 20 Copynumber: 4.1 Consensus size: 19
39701 AATAACCAAT
*
39711 ATGTCCCGAAGGACCACTG
1 ATGTTCCGAAGGACCACTG
*
39730 ACTGTTCCGAAGAACCACT-
1 A-TGTTCCGAAGGACCACTG
*
39749 ATGTCCCGAAGGACCACTG
1 ATGTTCCGAAGGACCACTG
*
39768 -TTTGTCTCGAAGGACCACTG
1 ATGT-TC-CGAAGGACCACTG
39788 AT
1 AT
39790 AATCCCTCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
18 17 0.35
19 3 0.06
20 28 0.57
21 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.22
Consensus pattern (19 bp):
ATGTTCCGAAGGACCACTG
Found at i:39779 original size:38 final size:38
Alignment explanation
Indices: 39692--39786 Score: 129
Period size: 38 Copynumber: 2.5 Consensus size: 38
39682 GCACTGAATA
* *
39692 TTTGTCTCGAATAACCAATATGTCCCGAAGGACCACTG
1 TTTGTCTCGAAGAACCACTATGTCCCGAAGGACCACTG
**
39730 ACTGT-TCCGAAGAACCACTATGTCCCGAAGGACCACTG
1 TTTGTCT-CGAAGAACCACTATGTCCCGAAGGACCACTG
*
39768 TTTGTCTCGAAGGACCACT
1 TTTGTCTCGAAGAACCACT
39787 GATAATCCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 1 0.02
38 46 0.96
39 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
TTTGTCTCGAAGAACCACTATGTCCCGAAGGACCACTG
Found at i:40753 original size:2 final size:2
Alignment explanation
Indices: 40746--40782 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
40736 TCACATGAAT
40746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40783 GATTTACTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42499 original size:77 final size:76
Alignment explanation
Indices: 42309--42673 Score: 379
Period size: 76 Copynumber: 4.9 Consensus size: 76
42299 GTGTTACAAT
* * *
42309 TTACATTATTATTATGCCTTTAAACAACCTGGTAGCTAGTTTAACGTAATAAGTTACACTTATTT
1 TTACATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAAGTTGCACTTATTT
42374 TATTTTA-CTGG
66 TATTTTACCT-G
* * * * *
42385 TTACATTATTATTATATCGTTAAACAAACTGTTAGCTAGTTTAACGTAATATGTTGCATTTA-TT
1 TTACATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAAGTTGCACTTATTT
42449 T-TTTTACCTG
66 TATTTTACCTG
* *
42459 TTACATTAATATTATTATACCTTTAAACAAACAT-GTAGCTAGTTTAACGTAATAAGTTGCGCCT
1 TTACA-T--TATTATTATACCTTTAAACAAAC-TGGTAGCTAGTTTAACGTAATAAGTTGCACTT
42523 ATTTTATTTTACC-G
62 ATTTTATTTTACCTG
* * *
42537 TTTACATTATTATTATGCCTTTAAACAAATTGGTAGCTAG-TT----T--T--G-CGC-C-TATT
1 -TTACATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAAGTTGCACTTATT
42590 TTATTTTACCGT-
65 TTATTTTACC-TG
* * * * *
42602 TTACATTATTATTATACATTTAAACAAACCGATAGCTAGTTTAACGTAATATGTTGCACCTATTT
1 TTACATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAAGTTGCACTTATTT
42667 TATTTTA
66 TATTTTA
42674 ATCGGTTAAG
Statistics
Matches: 242, Mismatches: 24, Indels: 46
0.78 0.08 0.15
Matches are distributed among these distances:
64 48 0.20
65 3 0.01
66 2 0.01
67 1 0.00
69 2 0.01
71 2 0.01
73 1 0.00
74 13 0.05
75 10 0.04
76 95 0.39
77 47 0.19
78 6 0.02
79 12 0.05
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (76 bp):
TTACATTATTATTATACCTTTAAACAAACTGGTAGCTAGTTTAACGTAATAAGTTGCACTTATTT
TATTTTACCTG
Found at i:42616 original size:64 final size:64
Alignment explanation
Indices: 42515--42643 Score: 213
Period size: 64 Copynumber: 2.0 Consensus size: 64
42505 ACGTAATAAG
* * ** *
42515 TTGCGCCTATTTTATTTTACCGTTTACATTATTATTATGCCTTTAAACAAATTGGTAGCTAGTT
1 TTGCGCCTATTTTATTTTACCGTTTACATTATTATTATACATTTAAACAAACCGATAGCTAGTT
42579 TTGCGCCTATTTTATTTTACCGTTTACATTATTATTATACATTTAAACAAACCGATAGCTAGTT
1 TTGCGCCTATTTTATTTTACCGTTTACATTATTATTATACATTTAAACAAACCGATAGCTAGTT
42643 T
1 T
42644 AACGTAATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (64 bp):
TTGCGCCTATTTTATTTTACCGTTTACATTATTATTATACATTTAAACAAACCGATAGCTAGTT
Found at i:42712 original size:99 final size:99
Alignment explanation
Indices: 42591--42897 Score: 442
Period size: 99 Copynumber: 3.1 Consensus size: 99
42581 GCGCCTATTT
* * *
42591 TATTTTACCGTTTACATTATTATTATACATTTAAACAAACCGATAGCTAGTTTAACGTAATATGT
1 TATTTTACAGTTTACATTATTATTATAC-TTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGT
42656 TGCACCTATTTTATTTTAATCGGTTAAGTTGTAAA
65 TGCACCTATTTTATTTTAATCGGTTAAGTTGTAAA
42691 T-TTTTACAGTTTACATTATTATTATATCTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGT
1 TATTTTACAGTTTACATTATTATTATA-CTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGT
*
42755 TGCACCTATTTTATTTT-AGCTGGTTAAGTTG-AAA
65 TGCACCTATTTTATTTTAATC-GGTTAAGTTGTAAA
* * * *
42789 TATTTTATAGTTTACGTTATTATTATACCTTTAAACAAATCGGTAGCCAGTTTAACGTAATAGGT
1 TATTTTACAGTTTACATTATTATTATA-CTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGT
* * *
42854 TGCACATATTTTATTTTAATC-GTTAAGCTGTAAT
65 TGCACCTATTTTATTTTAATCGGTTAAGTTGTAAA
42888 TATTATTACA
1 TATT-TTACA
42898 CTATTGATAT
Statistics
Matches: 187, Mismatches: 14, Indels: 12
0.88 0.07 0.06
Matches are distributed among these distances:
98 14 0.07
99 165 0.88
100 8 0.04
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (99 bp):
TATTTTACAGTTTACATTATTATTATACTTTAAACAAACCGGTAGCTAGTTTAACGTAATAGGTT
GCACCTATTTTATTTTAATCGGTTAAGTTGTAAA
Found at i:43293 original size:71 final size:71
Alignment explanation
Indices: 43100--43335 Score: 220
Period size: 72 Copynumber: 3.4 Consensus size: 71
43090 ATCATATTGT
* * *
43100 AGTATTAATATTTATTAAAAAA-ATTGATACTTTACA-TTCTTCTCATTTTCTATGTTCTTTTTT
1 AGTATTAATATTTGTGAAAAAATATTGATACTTTACAGCT-TTCTCATTTTC-ATGTT-TTTTTT
43163 TAATTCGAA
63 TAATTCGAA
* * * * *
43172 AGTATTGATGTTTGTG-GAAAATATTGAAACTTTGCAGAC-TTCTCATTTTTCATGTTTTTTTTT
1 AGTATTAATATTTGTGAAAAAATATTGATACTTTACAG-CTTTCTCA-TTTTCATGTTTTTTTTT
* *
43235 AATTTGGA
64 AATTCGAA
*
43243 AGTATCAATATTTGTGAAAAAATATTGATACTTTACAGCTTTCTCATTTTCCA----TTTTTTTA
1 AGTATTAATATTTGTGAAAAAATATTGATACTTTACAGCTTTCTCATTTT-CATGTTTTTTTTTA
43304 ATTCGAA
65 ATTCGAA
* * *
43311 AATATCT-ATACTTGTGGAAAAATAT
1 AGTAT-TAATATTTGTGAAAAAATAT
43336 AAATATTTAC
Statistics
Matches: 134, Mismatches: 22, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
68 33 0.25
71 35 0.26
72 61 0.46
73 5 0.04
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (71 bp):
AGTATTAATATTTGTGAAAAAATATTGATACTTTACAGCTTTCTCATTTTCATGTTTTTTTTTAA
TTCGAA
Found at i:50802 original size:16 final size:16
Alignment explanation
Indices: 50781--50813 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
50771 TAATAAATAA
50781 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
50797 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
50813 A
1 A
50814 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:50903 original size:16 final size:16
Alignment explanation
Indices: 50882--50931 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
50872 TAATAAATAA
50882 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
50898 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
50914 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
50930 AC
1 AC
50932 AAACGTTGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:51981 original size:24 final size:24
Alignment explanation
Indices: 51954--52015 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
51944 TATTGGGTTA
* *
51954 AACATAAATGAATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
51978 AACATAACCGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
*
52002 AACATAACCGAACG
1 AACATAAACGAACG
52016 TTTACGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.55, C:0.21, G:0.13, T:0.11
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:51982 original size:10 final size:10
Alignment explanation
Indices: 51967--52014 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
51957 ATAAATGAAT
51967 GAACATAAAC
1 GAACATAAAC
51977 GAACATAACCGAAC
1 GAACAT-A---AAC
51991 GAACATAAAC
1 GAACATAAAC
*
52001 GAACATAACC
1 GAACATAAAC
52011 GAAC
1 GAAC
52015 GTTTACGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:51991 original size:14 final size:14
Alignment explanation
Indices: 51974--52015 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
51964 AATGAACATA
51974 AACGAACATAACCG
1 AACGAACATAACCG
51988 AACGAACAT-A---
1 AACGAACATAACCG
51998 AACGAACATAACCG
1 AACGAACATAACCG
52012 AACG
1 AACG
52016 TTTACGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:56975 original size:2 final size:2
Alignment explanation
Indices: 56970--57007 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
56960 ATAAAAGTTA
*
56970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57008 GAAAAAAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57590 original size:21 final size:21
Alignment explanation
Indices: 57473--57610 Score: 77
Period size: 21 Copynumber: 6.7 Consensus size: 21
57463 ATGCGAAATA
**
57473 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
57493 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
57513 AAAATAGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
57534 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
57555 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * *
57576 AAAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
57596 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
57611 ACACATAAAT
Statistics
Matches: 87, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.44
21 46 0.53
22 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:57639 original size:20 final size:20
Alignment explanation
Indices: 57577--57806 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
57567 CGATTTTCCA
* ** *
57577 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
57597 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
57617 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
57637 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
57657 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
57677 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
57697 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
57717 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
57737 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
57757 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
57777 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
57797 AAATCACAAC
1 AAATCGCAAC
57807 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:58500 original size:24 final size:24
Alignment explanation
Indices: 58468--58522 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
58458 GTGAGTACTA
* * *
58468 GTCAGTATTCGAAATTTGGTCTTG
1 GTCAATATTCGAAATTTGATATTG
* *
58492 GTCAATATTCGGACTTTGATATTG
1 GTCAATATTCGAAATTTGATATTG
58516 GTCAATA
1 GTCAATA
58523 CACGGATTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.40
Consensus pattern (24 bp):
GTCAATATTCGAAATTTGATATTG
Found at i:58528 original size:24 final size:24
Alignment explanation
Indices: 58489--58535 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
58479 AAATTTGGTC
**
58489 TTGGTCAATATTCGGACTTTGATA
1 TTGGTCAATACACGGACTTTGATA
*
58513 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
58536 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:58727 original size:12 final size:12
Alignment explanation
Indices: 58710--58734 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58700 ATATAATCCT
58710 GAAGAAGAAAAA
1 GAAGAAGAAAAA
58722 GAAGAAGAAAAA
1 GAAGAAGAAAAA
58734 G
1 G
58735 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:61021 original size:33 final size:33
Alignment explanation
Indices: 60979--61066 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
60969 TGTTATCACT
60979 ATTTTGGTTTCGCGTTGCGA-TCTTGTCGTTGCG
1 ATTTTGGTTTCGCGTTGCGATTC-TGTCGTTGCG
61012 ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
1 ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
**
61045 ATTTTCATTTCGCGTTGCGATT
1 ATTTTGGTTTCGCGTTGCGATT
61067 TTGGTTTCGC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 50 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.27, T:0.47
Consensus pattern (33 bp):
ATTTTGGTTTCGCGTTGCGATTCTGTCGTTGCG
Found at i:61029 original size:19 final size:19
Alignment explanation
Indices: 60979--61103 Score: 117
Period size: 19 Copynumber: 7.1 Consensus size: 19
60969 TGTTATCACT
60979 ATTTTGGTTTCGCGTTGCG
1 ATTTTGGTTTCGCGTTGCG
*
60998 ATCTT-G--T--CGTTGCG
1 ATTTTGGTTTCGCGTTGCG
61012 ATTTTGGTTTCGCGTTGCG
1 ATTTTGGTTTCGCGTTGCG
*
61031 ATTCT-G--T--CGTTGCG
1 ATTTTGGTTTCGCGTTGCG
**
61045 ATTTTCATTTCGCGTTGCG
1 ATTTTGGTTTCGCGTTGCG
61064 ATTTTGGTTTCGCGTTGCG
1 ATTTTGGTTTCGCGTTGCG
* *
61083 ATTTTAAGTTTCGTGTTGCG
1 ATTTT-GGTTTCGCGTTGCG
61103 A
1 A
61104 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
14 22 0.26
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 44 0.51
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
ATTTTGGTTTCGCGTTGCG
Found at i:61267 original size:93 final size:93
Alignment explanation
Indices: 61151--61543 Score: 468
Period size: 93 Copynumber: 4.1 Consensus size: 93
61141 ATGGATTGCA
61151 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
61215 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
61243 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTG
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGT-
* * * * *
61308 TTAAAGAATACACAGTTTAGCAG-AATTGGCAGCAACCGAA-
65 TT--AG----CAGA-ATTGGCAGCAA----CCG-AA-CAAAT
** * *** * *
61348 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACA
1 TTACTTT-CAACCAA-AAGA---CAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACA
61413 CAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
61 CAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
61446 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
61511 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
61539 TTACT
1 TTACT
61544 AAGCAATCTA
Statistics
Matches: 252, Mismatches: 27, Indels: 43
0.78 0.08 0.13
Matches are distributed among these distances:
92 4 0.02
93 138 0.55
94 2 0.01
96 4 0.02
97 7 0.03
98 6 0.02
99 2 0.01
100 5 0.02
101 6 0.02
102 6 0.02
103 5 0.02
104 2 0.01
105 6 0.02
106 7 0.03
107 4 0.02
109 2 0.01
110 46 0.18
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:61333 original size:17 final size:17
Alignment explanation
Indices: 61284--61323 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
61274 AATACTATTT
61284 CACAGTGTTAAAGAATA
1 CACAGTGTTAAAGAATA
61301 CACAGTGTTAAAGAATA
1 CACAGTGTTAAAGAATA
61318 CACAGT
1 CACAGT
61324 TTAGCAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (17 bp):
CACAGTGTTAAAGAATA
Found at i:61426 original size:110 final size:110
Alignment explanation
Indices: 61191--61416 Score: 452
Period size: 110 Copynumber: 2.1 Consensus size: 110
61181 AATACTATTT
61191 CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCA
1 CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCA
61256 AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATA
66 AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATA
61301 CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCA
1 CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCA
61366 AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATA
66 AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATA
61411 CACAGT
1 CACAGT
61417 TTAGCAGAAT
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 116 1.00
ACGTcount: A:0.46, C:0.19, G:0.14, T:0.22
Consensus pattern (110 bp):
CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCA
AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATA
Found at i:63269 original size:14 final size:14
Alignment explanation
Indices: 63250--63306 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
63240 TTGAAATGAA
63250 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
63264 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
63283 AATCGCAACGAGAG
1 AATCGCAACGAGAG
63297 AATCGCAACG
1 AATCGCAACG
63307 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.42, C:0.25, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:63287 original size:33 final size:33
Alignment explanation
Indices: 63242--63325 Score: 159
Period size: 33 Copynumber: 2.5 Consensus size: 33
63232 TCTTTTGGTT
63242 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
63275 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
63308 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
63326 CGAAATGAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:63288 original size:19 final size:19
Alignment explanation
Indices: 63264--63347 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
63254 GCAACGAGAG
*
63264 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
63283 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
63297 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
63316 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
63335 AATCGCAATGCGA
1 AATCGCAACGCGA
63348 TTTTGGTTTC
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:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:63378 original size:14 final size:14
Alignment explanation
Indices: 63359--63415 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
63349 TTTGGTTTCG
63359 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
63373 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
63392 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
63406 CGTTGCGATT
1 CGTTGCGATT
63416 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:63391 original size:33 final size:33
Alignment explanation
Indices: 63343--63423 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
63333 AAAATCGCAA
**
63343 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
63376 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
63409 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
63424 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:63426 original size:21 final size:21
Alignment explanation
Indices: 63400--63475 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
63390 CGCGTTGCGA
63400 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
63421 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
63441 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
63462 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
63476 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:63456 original size:41 final size:41
Alignment explanation
Indices: 63399--63476 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
63389 TCGCGTTGCG
*
63399 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
63440 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
63477 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:63597 original size:33 final size:33
Alignment explanation
Indices: 63555--63625 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
63545 AATACTAACT
*
63555 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
63588 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
63621 TGAAA
1 TGAAA
63626 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:63859 original size:22 final size:22
Alignment explanation
Indices: 63807--63861 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
63797 TGGTTGTGAG
*
63807 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
63829 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
63851 GGATTTCTTCG
1 GGATTTCTTCG
63862 CCGTAGAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:64033 original size:20 final size:20
Alignment explanation
Indices: 64008--64201 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
63998 CTTTAAATAT
64008 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
64028 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
64050 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
64069 TGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
64089 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
*
64109 CGCGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
64129 CACGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
64149 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
64169 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
64189 CGCGTTGCGATTT
1 CGCGTTGCGATTT
64202 TGGAAAATCG
Statistics
Matches: 142, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 123 0.87
21 15 0.11
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:64173 original size:60 final size:60
Alignment explanation
Indices: 64010--64181 Score: 218
Period size: 60 Copynumber: 2.9 Consensus size: 60
64000 TTAAATATCG
** **
64010 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATATG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** * *
64071 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGTGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
* *
64131 CGTTACGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
64182 TCATATTCGC
Statistics
Matches: 91, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 65 0.71
61 26 0.29
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:64218 original size:21 final size:21
Alignment explanation
Indices: 64188--64270 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
64178 ATTTTCATAT
*
64188 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
64209 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
64230 TCGCATTGCAATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
64251 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
64271 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:65548 original size:19 final size:18
Alignment explanation
Indices: 65524--65562 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
65514 AAATAAAAAG
* *
65524 ATTTAAATATTAAAATCGT
1 ATTTAAACACTAAAAT-GT
65543 ATTTAAACACTAAAATGT
1 ATTTAAACACTAAAATGT
65561 AT
1 AT
65563 AATTACCCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (18 bp):
ATTTAAACACTAAAATGT
Found at i:74473 original size:29 final size:27
Alignment explanation
Indices: 74417--74475 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
74407 TTTTTGGATT
* *
74417 TTATTTTGATTAAAAAATGTTACACAC
1 TTATTTTGATAAAAAAATGTTAAACAC
*
74444 TTATTTTGATCAAAATAAATTTTAAACAC
1 TTATTTTGAT-AAAA-AAATGTTAAACAC
74473 TTA
1 TTA
74476 AATAAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 10 0.37
28 3 0.11
29 14 0.52
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (27 bp):
TTATTTTGATAAAAAAATGTTAAACAC
Found at i:82689 original size:2 final size:2
Alignment explanation
Indices: 82682--82709 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
82672 AACTCATCGG
82682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
82710 CTGTGGTGGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:82829 original size:41 final size:41
Alignment explanation
Indices: 82772--82863 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
82762 GATCTTTCTT
* * *
82772 TTTATTTTATTGATTGTATCCGTCTTAAAAATTTA-TTTGTG
1 TTTATTTTGTTGATTGTATCCATCCT-AAAATTTAGTTTGTG
*
82813 TTTATTTTGTTGATTGTGTCCATCCTAAAATTTAGTTTGTG
1 TTTATTTTGTTGATTGTATCCATCCTAAAATTTAGTTTGTG
* *
82854 CTTAGTTTGT
1 TTTATTTTGT
82864 ATACAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
40 8 0.18
41 36 0.82
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.55
Consensus pattern (41 bp):
TTTATTTTGTTGATTGTATCCATCCTAAAATTTAGTTTGTG
Found at i:83503 original size:15 final size:16
Alignment explanation
Indices: 83480--83513 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
83470 AATATATATA
83480 AATTAATAAATT-ATT
1 AATTAATAAATTAATT
*
83495 AATTTATAAATTAATT
1 AATTAATAAATTAATT
83511 AAT
1 AAT
83514 ATCTCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAATAAATTAATT
Found at i:88887 original size:3 final size:3
Alignment explanation
Indices: 88879--88906 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
88869 TGCCGTAACA
88879 GTG GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG G
88907 AGATAGAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:89034 original size:21 final size:21
Alignment explanation
Indices: 89010--89062 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
89000 AATTACATTG
*
89010 TGTGGTGATG-AAGTGAATGGA
1 TGTGATGATGTAA-TGAATGGA
*
89031 TGTGATGATGTTATGAATGGA
1 TGTGATGATGTAATGAATGGA
89052 TGTGATGATGT
1 TGTGATGATGT
89063 TGAAGGTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.38, T:0.36
Consensus pattern (21 bp):
TGTGATGATGTAATGAATGGA
Found at i:89063 original size:21 final size:21
Alignment explanation
Indices: 89023--89063 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
89013 GGTGATGAAG
89023 TGAATGGATGTGATGATGTTA
1 TGAATGGATGTGATGATGTTA
89044 TGAATGGATGTGATGATGTT
1 TGAATGGATGTGATGATGTT
89064 GAAGGTGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (21 bp):
TGAATGGATGTGATGATGTTA
Found at i:93654 original size:20 final size:19
Alignment explanation
Indices: 93626--93663 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
93616 GAAATATAAT
93626 AAATAATAATATTCATTATA
1 AAATAATAATA-TCATTATA
*
93646 AAATCATAATATCATTAT
1 AAATAATAATATCATTAT
93664 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATAATAATATCATTATA
Found at i:96049 original size:17 final size:18
Alignment explanation
Indices: 96011--96049 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
96001 TGATTTAATT
96011 TTTAATTCAAATACTTAA
1 TTTAATTCAAATACTTAA
*
96029 -TTAATTCAAAT-TTTAA
1 TTTAATTCAAATACTTAA
96045 TTTAA
1 TTTAA
96050 AATTATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAATTCAAATACTTAA
Found at i:96793 original size:2 final size:2
Alignment explanation
Indices: 96786--96816 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
96776 CTTTAAAACT
96786 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
96817 TACATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:97799 original size:14 final size:14
Alignment explanation
Indices: 97780--97815 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
97770 TAAAATAAAT
*
97780 TATATTTTTTGAAA
1 TATATTTTCTGAAA
97794 TATATTTTCTGAAA
1 TATATTTTCTGAAA
*
97808 AATATTTT
1 TATATTTT
97816 ACTATATTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (14 bp):
TATATTTTCTGAAA
Found at i:97926 original size:22 final size:21
Alignment explanation
Indices: 97901--97982 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 21
97891 TACAATAAAT
97901 ATATTATTTATCATAAAATTTA
1 ATATTATTTAT-ATAAAATTTA
*
97923 ATATTATTATTTATAAAATATTA
1 ATATTATT-TATATAAAAT-TTA
* * * *
97946 AAATAATTTATATAATATTAAA
1 ATATTATTTATATAAAATT-TA
*
97968 ATATTATTTTTATAA
1 ATATTATTTATATAA
97983 TTTTATTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.02
22 36 0.75
23 11 0.23
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTATTTATATAAAATTTA
Found at i:97983 original size:22 final size:22
Alignment explanation
Indices: 97896--97983 Score: 90
Period size: 20 Copynumber: 3.9 Consensus size: 22
97886 TTAAATACAA
*
97896 TAAATATATTATTTATCATAAAATT
1 TAAA-ATATTATTTAT-ATAATA-T
* *
97921 TAATATTATTATTTATAAAATAT
1 TAA-AATATTATTTATATAATAT
97944 TAAAATA--ATTTATATAATAT
1 TAAAATATTATTTATATAATAT
*
97964 TAAAATATTATTTTTATAAT
1 TAAAATATTATTTATATAAT
97984 TTTATTAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
20 19 0.35
22 13 0.24
23 4 0.07
24 4 0.07
25 13 0.24
26 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAAATATTATTTATATAATAT
Found at i:97993 original size:31 final size:32
Alignment explanation
Indices: 97948--98037 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 32
97938 AAATATTAAA
*
97948 ATAA-TTTATATAATATTAAAATATTAT-TT-TT
1 ATAATTTTAT-TAATA-TAAAATATTATATTGGT
97979 ATAATTTTATTAATA-AAAATATTAATATTGGT
1 ATAATTTTATTAATATAAAATATT-ATATTGGT
98011 AT-ATTTTATTGAA-ATAAAAATATTATA
1 ATAATTTTATT-AATAT-AAAATATTATA
98038 AATTATATTA
Statistics
Matches: 51, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
29 8 0.16
30 2 0.04
31 20 0.39
32 13 0.25
33 8 0.16
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (32 bp):
ATAATTTTATTAATATAAAATATTATATTGGT
Found at i:98045 original size:31 final size:29
Alignment explanation
Indices: 97923--98046 Score: 73
Period size: 31 Copynumber: 4.2 Consensus size: 29
97913 ATAAAATTTA
*
97923 ATATTATTATTTAT-AAAATATTAA-AA-T
1 ATATT-TTATTAATAAAAATATTAATAATT
**
97950 A-A-TTTATATAATATTAAAATATT-ATTTTT
1 ATATTTTAT-TAATA--AAAATATTAATAATT
*
97979 ATAATTTTATTAATAAAAATATTAATATTGGT
1 AT-ATTTTATTAATAAAAATATTAATAAT--T
98011 ATATTTTATTGAAATAAAAATATT-ATAAATT
1 ATATTTTATT--AATAAAAATATTAAT-AATT
98042 ATATT
1 ATATT
98047 AATTATTTAT
Statistics
Matches: 77, Mismatches: 5, Indels: 26
0.71 0.05 0.24
Matches are distributed among these distances:
24 4 0.05
25 4 0.05
26 1 0.01
27 2 0.03
28 8 0.10
29 10 0.13
30 4 0.05
31 20 0.26
32 10 0.13
33 14 0.18
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
ATATTTTATTAATAAAAATATTAATAATT
Found at i:98106 original size:22 final size:22
Alignment explanation
Indices: 98076--98119 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
98066 AGTGTTATAT
98076 TATAATTTAAAAATATTAATTA
1 TATAATTTAAAAATATTAATTA
* * *
98098 TATATTTTAAATATATTTATTA
1 TATAATTTAAAAATATTAATTA
98120 AAATATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATAATTTAAAAATATTAATTA
Found at i:98169 original size:27 final size:27
Alignment explanation
Indices: 98139--98194 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
98129 TAGATTATTA
98139 TATT-AATATTAA-ATATATAGATAATAT
1 TATTCAATATTAATA-ATATA-ATAATAT
* *
98166 TATTCATTATTAATAATTTAATAATAT
1 TATTCAATATTAATAATATAATAATAT
98193 TA
1 TA
98195 CTTCTATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 13 0.52
28 11 0.44
29 1 0.04
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
TATTCAATATTAATAATATAATAATAT
Found at i:98328 original size:22 final size:22
Alignment explanation
Indices: 98300--98345 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
98290 TTGATTATTT
98300 TATTATAATATTAAAA-ATATAA
1 TATTATAATATTAAAATAT-TAA
*
98322 TATTATATTATTAAAATATTAA
1 TATTATAATATTAAAATATTAA
98344 TA
1 TA
98346 AATATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTATAATATTAAAATATTAA
Found at i:98333 original size:30 final size:33
Alignment explanation
Indices: 98273--98351 Score: 101
Period size: 30 Copynumber: 2.5 Consensus size: 33
98263 ATAATATCTT
* * *
98273 ATATTATTATAATATAATTGATTATTTTATTATA
1 ATATTAATA-AATATAATTGATTATATTATTAAA
98307 ATATTAA-AAATATAA-T-ATTATATTATTAAA
1 ATATTAATAAATATAATTGATTATATTATTAAA
98337 ATATTAATAAATATA
1 ATATTAATAAATATA
98352 TTTTTAGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 19 0.46
31 8 0.20
32 7 0.17
33 1 0.02
34 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (33 bp):
ATATTAATAAATATAATTGATTATATTATTAAA
Found at i:98354 original size:55 final size:52
Alignment explanation
Indices: 98241--98355 Score: 135
Period size: 55 Copynumber: 2.2 Consensus size: 52
98231 AATAATTTAT
* * **
98241 TATATATTATTAAAATAAAAATATAATATCTTATATTATTATAATATAATTGA
1 TATATTTTATTAAAATAAAAATATAATA-CTTATATTATTAAAATATAATAAA
98294 T-TATTTTATTATAATATTAAAAATATAATA-TTATATTATTAAAATATTAATAAA
1 TATATTTTATTA-AA-A-TAAAAATATAATACTTATATTATTAAAATA-TAATAAA
98348 TATATTTT
1 TATATTTT
98356 TAGATATTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
52 9 0.17
53 18 0.34
54 7 0.13
55 19 0.36
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TATATTTTATTAAAATAAAAATATAATACTTATATTATTAAAATATAATAAA
Found at i:98386 original size:11 final size:11
Alignment explanation
Indices: 98370--98412 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
98360 TATTTTAATA
98370 ATTAATATTTT
1 ATTAATATTTT
**
98381 ATTAATATGAT
1 ATTAATATTTT
*
98392 ATTAAATGTTTT
1 ATT-AATATTTT
98404 ATTAATATT
1 ATTAATATT
98413 AAATTCATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 17 0.68
12 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (11 bp):
ATTAATATTTT
Found at i:105041 original size:2 final size:2
Alignment explanation
Indices: 105034--105069 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
105024 AAATAATAAA
105034 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
105070 GTGTAGGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107148 original size:12 final size:12
Alignment explanation
Indices: 107126--107153 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
107116 TTCCTCCAAC
107126 CCCACCTCCAGT
1 CCCACCTCCAGT
107138 CCCACCTCCAGT
1 CCCACCTCCAGT
107150 CCCA
1 CCCA
107154 AGCCCTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.61, G:0.07, T:0.14
Consensus pattern (12 bp):
CCCACCTCCAGT
Done.