Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002840.1 Hibiscus syriacus cultivar Beakdansim tig00005846_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: 246210
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 2
Found at i:484 original size:47 final size:49
Alignment explanation
Indices: 433--526 Score: 147
Period size: 47 Copynumber: 1.9 Consensus size: 49
423 ACATATAAAG
*
433 AAAAAACATAATCATTACA-TAATCTTTTGGT-GTTTAATAAAAAATGA
1 AAAAAACATAATCATTACACCAATCTTTTGGTAGTTTAATAAAAAATGA
*
480 AAAAAACATAATCATTACACCAATCTTTTGGTAGGTTTAGTAAAAAA
1 AAAAAACATAATCATTACACCAATCTTTTGGTA-GTTTAATAAAAAA
527 ATGGTATATT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
47 19 0.45
48 11 0.26
50 12 0.29
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.32
Consensus pattern (49 bp):
AAAAAACATAATCATTACACCAATCTTTTGGTAGTTTAATAAAAAATGA
Found at i:767 original size:22 final size:22
Alignment explanation
Indices: 739--796 Score: 100
Period size: 21 Copynumber: 2.7 Consensus size: 22
729 TGTTTTACTT
739 TTTATAATTTTTTAAAATTGAG
1 TTTATAATTTTTTAAAATTGAG
*
761 TTTATAATTTTTT-AAATTGAT
1 TTTATAATTTTTTAAAATTGAG
782 TTTATAATTTTTTAA
1 TTTATAATTTTTTAA
797 TTATTATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTATAATTTTTTAAAATTGAG
Found at i:769 original size:12 final size:12
Alignment explanation
Indices: 738--790 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 12
728 TTGTTTTACT
738 TTTTATAATT--
1 TTTTATAATTGA
*
748 TTTTAAAATTGA
1 TTTTATAATTGA
*
760 GTTTATAATT--
1 TTTTATAATTGA
770 TTTTA-AATTGA
1 TTTTATAATTGA
781 TTTTATAATT
1 TTTTATAATT
791 TTTTAATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 4 0.12
10 13 0.38
11 5 0.15
12 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (12 bp):
TTTTATAATTGA
Found at i:957 original size:28 final size:26
Alignment explanation
Indices: 922--979 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
912 TTTAACAAAA
* * *
922 TTTAAAATTTAGTAATTATTTTATAACT
1 TTTAAAATTAAATAA-TAATTTATAA-T
950 TTTAAAATTAAATAATAATTTATAAT
1 TTTAAAATTAAATAATAATTTATAAT
976 TTTA
1 TTTA
980 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 5 0.19
27 9 0.33
28 13 0.48
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAAAATTAAATAATAATTTATAAT
Found at i:1896 original size:33 final size:33
Alignment explanation
Indices: 1854--1922 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1844 ATGATAATGC
1854 ATAAAAATCCCCCTTAGGTTCCTGGACTAAGTA
1 ATAAAAATCCCCCTTAGGTTCCTGGACTAAGTA
1887 ATAAAAATCCCCCTTAGGTTCCTGGACTAAGTA
1 ATAAAAATCCCCCTTAGGTTCCTGGACTAAGTA
1920 ATA
1 ATA
1923 TTGCCTTGGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (33 bp):
ATAAAAATCCCCCTTAGGTTCCTGGACTAAGTA
Found at i:7245 original size:15 final size:15
Alignment explanation
Indices: 7227--7257 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7217 AAATTCTAAA
7227 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
7242 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
7257 T
1 T
7258 CATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:9395 original size:26 final size:26
Alignment explanation
Indices: 9359--9414 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
9349 TTAGAGCATT
*
9359 TATTCAATAGGTAAACACATGAATCG
1 TATTCAATAGGCAAACACATGAATCG
9385 TATTCAATAGGCAAACACATGAATCG
1 TATTCAATAGGCAAACACATGAATCG
9411 TATT
1 TATT
9415 ATGGAAGTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (26 bp):
TATTCAATAGGCAAACACATGAATCG
Found at i:11339 original size:40 final size:40
Alignment explanation
Indices: 11284--11364 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
11274 TTGGCGTAAA
11284 GAATGATTATTTTACCATCTAAATCGACCCAGATCTGATG
1 GAATGATTATTTTACCATCTAAATCGACCCAGATCTGATG
11324 GAATGATTATTTTACCATCTAAATCGACCCAGATCTGATG
1 GAATGATTATTTTACCATCTAAATCGACCCAGATCTGATG
11364 G
1 G
11365 CTCATGATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (40 bp):
GAATGATTATTTTACCATCTAAATCGACCCAGATCTGATG
Found at i:21744 original size:20 final size:21
Alignment explanation
Indices: 21719--21770 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
21709 TTTTCCCAAT
*
21719 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
21739 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
21760 TCGCAATGCGA
1 TCGCAATGCGA
21771 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:21784 original size:20 final size:20
Alignment explanation
Indices: 21759--21893 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
21749 AATTGGGAAA
21759 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
21779 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
21799 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
21820 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
21840 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* ** *
21860 TTCGCAACACGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
21880 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
21894 TTTCAAAGCG
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 65 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:21803 original size:61 final size:61
Alignment explanation
Indices: 21756--21887 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
21746 GCGAATTGGG
* * * * *
21756 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
21817 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACACGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
21878 ATAATCGCAA
1 AAAATCGCAA
21888 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:22422 original size:20 final size:20
Alignment explanation
Indices: 22368--22426 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
22358 GCGATTCTCT
**
22368 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
22388 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
22408 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
22427 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:22617 original size:25 final size:24
Alignment explanation
Indices: 22563--22617 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
22553 TGTTTATTAT
* *
22563 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
22587 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
22613 TGTTT
1 TGTTT
22618 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:23766 original size:18 final size:18
Alignment explanation
Indices: 23745--23787 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
23735 TCCACTTCGG
*
23745 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
23763 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
23781 GAGCCAT
1 GAGCCAT
23788 TATCTGATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.26, C:0.44, G:0.16, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:24325 original size:19 final size:20
Alignment explanation
Indices: 24271--24337 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
24261 TAGTTTACTT
* *
24271 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
24291 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
24311 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
24330 TCGCAACG
1 TCGCAACG
24338 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:24345 original size:14 final size:14
Alignment explanation
Indices: 24326--24383 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
24316 ATGCGAAATG
24326 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
24340 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
24356 ATGAAATTGCAACGAC
1 A--AAATCGCAACGAC
24372 AAAATCGCAACG
1 AAAATCGCAACG
24384 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:24352 original size:33 final size:33
Alignment explanation
Indices: 24310--24400 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
24300 GGAAATGGCT
24310 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
24343 ATCGCAATGCGAAATG-AAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
24375 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
24401 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:24466 original size:19 final size:20
Alignment explanation
Indices: 24444--24486 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
24434 TGCGATTTTT
24444 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
24463 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
24483 ATTT
1 ATTT
24487 TTGCGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:24477 original size:20 final size:20
Alignment explanation
Indices: 24452--24498 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
24442 TTATTTCGCA
24452 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* **
24472 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGCCATTTCCGCG
24492 TTGCGAT
1 TTGCGAT
24499 TTTAAGTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:26386 original size:14 final size:14
Alignment explanation
Indices: 26367--26402 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
26357 ATTGTTTAAT
26367 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
26381 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
26395 TGATTTGT
1 TGATTTGT
26403 TTAATTGATG
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:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:26563 original size:19 final size:19
Alignment explanation
Indices: 26539--26606 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
26529 ATCGCAACGA
26539 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
26558 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
26577 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
26591 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
26607 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:26650 original size:20 final size:20
Alignment explanation
Indices: 26633--26720 Score: 108
Period size: 20 Copynumber: 4.4 Consensus size: 20
26623 CGATTTTCTA
26633 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
26653 GTTGCGATTTTTCA-TTTCAAC
1 GTTGCGA-TAGCCATTTTC-GC
26674 -TTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
26693 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
26713 GTTGCGAT
1 GTTGCGAT
26721 TTCCCCGTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.07
20 48 0.86
21 4 0.07
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:26986 original size:20 final size:21
Alignment explanation
Indices: 26943--27000 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
26933 ATTGCGATTT
*
26943 TCAGAATCTCGTTTCGA-AAG
1 TCAGAATCTCGTTGCGATAAG
26963 TCAGAATCTCGTTGCGATAA-
1 TCAGAATCTCGTTGCGATAAG
* * *
26983 TCAGTATCGCATTGCGAT
1 TCAGAATCTCGTTGCGAT
27001 TTTCCAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (21 bp):
TCAGAATCTCGTTGCGATAAG
Found at i:27037 original size:20 final size:21
Alignment explanation
Indices: 26989--27040 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
26979 ATAATCAGTA
*
26989 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
27010 TTGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
27030 TCGCATTGCGA
1 TCGCATTGCGA
27041 ATTAGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:27256 original size:12 final size:12
Alignment explanation
Indices: 27239--27264 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27229 CTCCGGCGAC
27239 ATCCGTTCCTAT
1 ATCCGTTCCTAT
27251 ATCCGTTCCTAT
1 ATCCGTTCCTAT
27263 AT
1 AT
27265 ACTTCCCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.31, G:0.08, T:0.42
Consensus pattern (12 bp):
ATCCGTTCCTAT
Found at i:27853 original size:24 final size:24
Alignment explanation
Indices: 27826--27879 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
27816 GTATTCGAAA
*
27826 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
27850 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
27874 TTTGAT
1 TTTGAT
27880 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:30394 original size:19 final size:19
Alignment explanation
Indices: 30372--30493 Score: 85
Period size: 19 Copynumber: 7.2 Consensus size: 19
30362 GGAAATTACT
30372 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
30391 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
30405 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
30424 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
30438 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
30457 ATCGCAAT--G--A-GGGA
1 ATCGCAATGCGAAATGAAA
30471 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
30490 ATCG
1 ATCG
30494 TAACGCGAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 30
0.64 0.10 0.25
Matches are distributed among these distances:
14 28 0.37
15 3 0.04
16 5 0.07
17 5 0.07
18 3 0.04
19 32 0.42
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:30414 original size:33 final size:33
Alignment explanation
Indices: 30372--30498 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
30362 GGAAATTACT
30372 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
30405 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
30437 TTTCGCAATGCGAAATGAAAATCGCAATGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
30471 ATCGCAATGCGAAATGAAAATCGTAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
30499 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:30479 original size:66 final size:66
Alignment explanation
Indices: 30373--30505 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
30363 GAAATTACTA
*
30373 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
30438 T
66 T
* * *
30439 TCGCAATGCGAAATGAAAATCGCAATGAGGGAATCGCAATGCGAAATGAAAATCGTAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
30504 T
66 T
30505 T
1 T
30506 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:30680 original size:14 final size:14
Alignment explanation
Indices: 30661--30699 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
30651 CATCAATTAA
30661 ACAAATCAATTTTT
1 ACAAATCAATTTTT
**
30675 ACAAATCACCTTTT
1 ACAAATCAATTTTT
30689 ACAAATCAATT
1 ACAAATCAATT
30700 AAACAATCAA
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:0.44, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:32110 original size:42 final size:41
Alignment explanation
Indices: 32051--32256 Score: 155
Period size: 42 Copynumber: 4.9 Consensus size: 41
32041 GTGAATCGGG
* * *
32051 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAATGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
32093 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
32135 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * * *
32177 CTTTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
32219 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
32257 GCGAGTCGGG
Statistics
Matches: 125, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
41 9 0.07
42 105 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:32192 original size:84 final size:84
Alignment explanation
Indices: 32081--32256 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
32071 CCTCTTCAAC
*
32081 GATGACAATGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
32146 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
*
32165 GATGACAGTGGCCTTTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
32230 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
32249 GATGACAG
1 GATGACAG
32257 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:32651 original size:91 final size:92
Alignment explanation
Indices: 32475--32659 Score: 295
Period size: 91 Copynumber: 2.0 Consensus size: 92
32465 ATTTCAAACT
32475 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACA-AGTTTAGC
32540 AGAATTGGCAGCAACCGAATAAATTTAC
65 AGAATTGGCAGCAACCGAATAAATTTAC
* *
32568 TTCAACCAAAAGACAAAACAAAAAGATAAATACTAACTTCACAGTGTT-AATAA-AC-AGTTTAG
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAATACAAGTTTAG
*
32630 CAGTATTGGCAGCAACCGAATAAATTTAC
64 CAGAATTGGCAGCAACCGAATAAATTTAC
32659 T
1 T
32660 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 36 0.41
93 21 0.24
94 4 0.05
95 26 0.30
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (92 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACAAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTTAC
Found at i:34427 original size:33 final size:33
Alignment explanation
Indices: 34370--34457 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
34360 ACGAGATAAT
34370 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
34404 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
34437 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
34458 AAATCACAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:34462 original size:19 final size:19
Alignment explanation
Indices: 34345--34490 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
34335 TCTTTTGGTT
*
34345 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
34364 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
34384 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
34402 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
34418 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
34435 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
34451 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
34470 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
34489 GA
1 GA
34491 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 41 0.41
20 27 0.27
21 2 0.02
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:34519 original size:19 final size:19
Alignment explanation
Indices: 34486--34530 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
34476 AAAATCGCAA
*
34486 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
34505 TGCGATTTTTATTTCGTGT
1 TGCGATTTTGATTTCGCGT
34524 TGCGATT
1 TGCGATT
34531 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:0.13, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:35149 original size:20 final size:20
Alignment explanation
Indices: 35124--35177 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
35114 GATTTTGTAT
35124 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
35144 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
35164 TATCGCATTGCGAT
1 TATCGCATTGCGAT
35178 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:38627 original size:16 final size:16
Alignment explanation
Indices: 38603--38633 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38593 TGTTGTCCGG
38603 TTTTCAGTGAGATTCC
1 TTTTCAGTGAGATTCC
*
38619 TTTTTAGTGAGATTC
1 TTTTCAGTGAGATTC
38634 AAGTCTTAAA
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:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTCAGTGAGATTCC
Found at i:43180 original size:14 final size:14
Alignment explanation
Indices: 43153--43192 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
43143 CCTTTTTGCA
43153 TTGCAT-TCACA-T
1 TTGCATCTCACATT
43165 TTGCATCTCTACATT
1 TTGCATCTC-ACATT
43180 TTGCATCT-ACATT
1 TTGCATCTCACATT
43193 ACAGTTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 6 0.24
13 7 0.28
14 3 0.12
15 9 0.36
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.45
Consensus pattern (14 bp):
TTGCATCTCACATT
Found at i:46139 original size:25 final size:25
Alignment explanation
Indices: 46072--46141 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
46062 TAAAGGGCAC
**
46072 CATTTTTC-AAAAAACCTCATCAAA
1 CATTTTTCAAAAAAATTTCATCAAA
* ****
46096 CATTCTTCAAAGTTCTTTCATCAAA
1 CATTTTTCAAAAAAATTTCATCAAA
46121 CATTTTTCAAAAAAATTTCAT
1 CATTTTTCAAAAAAATTTCAT
46142 TATTTAAAAT
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
24 7 0.21
25 26 0.79
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.37
Consensus pattern (25 bp):
CATTTTTCAAAAAAATTTCATCAAA
Found at i:46595 original size:30 final size:30
Alignment explanation
Indices: 46531--46598 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
46521 CTAAGTACCA
* * *
46531 AAATAGTATAGGGACTTGGCCACTAATGCC
1 AAATAGTAAAAGGACTTGGCCACCAATGCC
* **
46561 AAATAGTAAAAGGACTTGGCCACCCATGTT
1 AAATAGTAAAAGGACTTGGCCACCAATGCC
46591 AAATAGTA
1 AAATAGTA
46599 CAGGGACCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (30 bp):
AAATAGTAAAAGGACTTGGCCACCAATGCC
Found at i:46666 original size:15 final size:15
Alignment explanation
Indices: 46646--46675 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
46636 ATTTCATCTA
46646 CTATGATTGAAGATT
1 CTATGATTGAAGATT
46661 CTATGATTGAAGATT
1 CTATGATTGAAGATT
46676 GTTTACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (15 bp):
CTATGATTGAAGATT
Found at i:48236 original size:13 final size:13
Alignment explanation
Indices: 48220--48244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48210 AACACAAAGG
48220 AAAAAAAGAAAAT
1 AAAAAAAGAAAAT
48233 AAAAAAAGAAAA
1 AAAAAAAGAAAA
48245 CTTTCGAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.08, T:0.04
Consensus pattern (13 bp):
AAAAAAAGAAAAT
Found at i:49063 original size:7 final size:7
Alignment explanation
Indices: 49051--49079 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
49041 TTTTCTATAT
49051 TATTTTA
1 TATTTTA
49058 TATTTTA
1 TATTTTA
49065 TATTTTA
1 TATTTTA
49072 TATTTTA
1 TATTTTA
49079 T
1 T
49080 TAAATATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTTA
Found at i:53891 original size:19 final size:18
Alignment explanation
Indices: 53850--53903 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
53840 ATTTACGATG
53850 ATAGAAACATATATATTT
1 ATAGAAACATATATATTT
* * *
53868 GTAGAAATCTTATTTATTT
1 ATAGAAA-CATATATATTT
* *
53887 ATAGATATATATATATT
1 ATAGAAACATATATATT
53904 ATGAGCTATA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (18 bp):
ATAGAAACATATATATTT
Found at i:56166 original size:12 final size:12
Alignment explanation
Indices: 56145--56178 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
56135 ACCACATTTC
*
56145 CAATACCAAACA
1 CAATATCAAACA
56157 CAATATCAAACA
1 CAATATCAAACA
*
56169 CAATCTCAAA
1 CAATATCAAA
56179 ACTCGTAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:56540 original size:3 final size:3
Alignment explanation
Indices: 56532--56562 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
56522 ATATAACTCT
56532 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
56563 TCCCCGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:58636 original size:18 final size:18
Alignment explanation
Indices: 58613--58648 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
58603 AAGCAAAAAG
58613 AAATCAAAATCACAATCA
1 AAATCAAAATCACAATCA
*
58631 AAATCAAAATCCCAATCA
1 AAATCAAAATCACAATCA
58649 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCACAATCA
Found at i:58855 original size:20 final size:20
Alignment explanation
Indices: 58830--58898 Score: 111
Period size: 20 Copynumber: 3.5 Consensus size: 20
58820 TTGTGATTGT
*
58830 ACTTTCGCGTTGCGAATTTG
1 ACTTTCGCATTGCGAATTTG
58850 ACTTTCGCATTGCGAATTTG
1 ACTTTCGCATTGCGAATTTG
*
58870 ACTTTTGCATTGCGAATTTG
1 ACTTTCGCATTGCGAATTTG
*
58890 ACTATCGCA
1 ACTTTCGCA
58899 ACCATCGCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ACTTTCGCATTGCGAATTTG
Found at i:58935 original size:20 final size:20
Alignment explanation
Indices: 58910--58954 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
58900 CCATCGCAAC
58910 GCGAATTTGACTTTCACGTT
1 GCGAATTTGACTTTCACGTT
*
58930 GCGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCACGTT
58950 GCGAA
1 GCGAA
58955 AGTGTACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
GCGAATTTGACTTTCACGTT
Found at i:59119 original size:64 final size:64
Alignment explanation
Indices: 59013--59161 Score: 219
Period size: 64 Copynumber: 2.3 Consensus size: 64
59003 AATTTAAAAC
*
59013 AATAAATAAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AATAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
59077 AATAAATCAACTTTTACAAATCAATTAAACAAG-AAAAGAATAATTCTTATTTCCTCATCAATTA
1 AATAAATCAACTTTTACAAATCAATTAAACAAGCAAAA-AATAAGAATTATTTACACATCAATTA
*
59141 AACAAATCAACTTTTACAAAT
1 AATAAATCAACTTTTACAAAT
59162 AATCAACTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
63 4 0.05
64 73 0.95
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (64 bp):
AATAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:59167 original size:17 final size:17
Alignment explanation
Indices: 59145--59185 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
59135 CAATTAAACA
59145 AATCAACTTTTACAAAT
1 AATCAACTTTTACAAAT
59162 AATCAACTTTTACAAAT
1 AATCAACTTTTACAAAT
59179 ACATCAA
1 A-ATCAA
59186 TTTCACGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (17 bp):
AATCAACTTTTACAAAT
Found at i:60587 original size:42 final size:42
Alignment explanation
Indices: 60526--60643 Score: 164
Period size: 42 Copynumber: 2.8 Consensus size: 42
60516 TCGGGATCTC
* *
60526 GAACGGTGGGAGGGACCTCTTGAACGATAACAGGGGCCTCTT
1 GAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGCCTCTT
* *
60568 GAACGGTGGGAGGGGCCTCTTGAAGGATGATAGGGGCCTCTT
1 GAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGCCTCTT
* * * *
60610 GAACGATAGGAGAGGCCTATTGAACGATGACAGG
1 GAACGGTGGGAGGGGCCTCTTGAACGATGACAGG
60644 TGAATATGGC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.19
Consensus pattern (42 bp):
GAACGGTGGGAGGGGCCTCTTGAACGATGACAGGGGCCTCTT
Found at i:60626 original size:21 final size:21
Alignment explanation
Indices: 60534--60637 Score: 111
Period size: 21 Copynumber: 5.0 Consensus size: 21
60524 TCGAACGGTG
*
60534 GGAGGGACCTCTTGAACGATA
1 GGAGGGGCCTCTTGAACGATA
** * *
60555 ACAGGGGCCTCTTGAACGGTG
1 GGAGGGGCCTCTTGAACGATA
*
60576 GGAGGGGCCTCTTGAAGGAT-
1 GGAGGGGCCTCTTGAACGATA
*
60596 GATAGGGGCCTCTTGAACGATA
1 G-GAGGGGCCTCTTGAACGATA
* *
60618 GGAGAGGCCTATTGAACGAT
1 GGAGGGGCCTCTTGAACGAT
60638 GACAGGTGAA
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
20 1 0.01
21 65 0.97
22 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.20
Consensus pattern (21 bp):
GGAGGGGCCTCTTGAACGATA
Found at i:62165 original size:21 final size:21
Alignment explanation
Indices: 62141--62186 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
62131 CCATTGTCAT
62141 CACGTAAA-ACCTCTACCTCAC
1 CACGTAAAGACC-CTACCTCAC
* *
62162 CACGTAAAGACCGTACCTCAT
1 CACGTAAAGACCCTACCTCAC
62183 CACG
1 CACG
62187 CCATGCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.33, C:0.39, G:0.11, T:0.17
Consensus pattern (21 bp):
CACGTAAAGACCCTACCTCAC
Found at i:62179 original size:63 final size:63
Alignment explanation
Indices: 62090--62211 Score: 149
Period size: 63 Copynumber: 1.9 Consensus size: 63
62080 CGTAGAGCGG
* *
62090 CTACCTCATCACGTAAAGTAGATACCTCACCACATAAAGCACCATTGTCATCACGTAAAACCT
1 CTACCTCACCACGTAAAGTAGATACCTCACCACACAAAGCACCATTGTCATCACGTAAAACCT
* * * * *
62153 CTACCTCACCACGTAAAG-ACCG-TACCTCATCACGCCATGCACCATTGTCTTCACGTAAA
1 CTACCTCACCACGTAAAGTA--GATACCTCACCACACAAAGCACCATTGTCATCACGTAAA
62212 GCACCGACTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 1 0.02
63 48 0.96
64 1 0.02
ACGTcount: A:0.33, C:0.34, G:0.11, T:0.22
Consensus pattern (63 bp):
CTACCTCACCACGTAAAGTAGATACCTCACCACACAAAGCACCATTGTCATCACGTAAAACCT
Found at i:64388 original size:19 final size:20
Alignment explanation
Indices: 64366--64403 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
64356 AATATTGTGT
64366 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
64385 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
64404 CGCGCTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:64496 original size:21 final size:21
Alignment explanation
Indices: 64472--64512 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
64462 GATTCACGTT
*
64472 GCGAATTTGGAAAATCGCAAC
1 GCGAATTCGGAAAATCGCAAC
64493 GCGAATTCGGAAAATCGCAA
1 GCGAATTCGGAAAATCGCAA
64513 TGTGATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTCGGAAAATCGCAAC
Found at i:64952 original size:70 final size:68
Alignment explanation
Indices: 64877--65105 Score: 221
Period size: 70 Copynumber: 3.3 Consensus size: 68
64867 AACAAGATAG
* *
64877 TCTCACTTGAGATATTTTCCTTTAAATTTTTTGTCTCACTCGGGACAGCTTCATTTGAAACAAAA
1 TCTCACTTGAGATATTTTCCTTTAAATTTTTTGTCTCACTAGAGACAG-TTC-TTTGAAACAAAA
64942 TTACA
64 TTACA
* * ** * *
64947 TCTCACTTGAGATATTTTCCCTTAAACGTTTTTGTCTC-CTTAGAGATGGTTTCTCT-AAAAAAA
1 TCTCACTTGAGATATTTTCCTTTAAA-TTTTTTGTCTCAC-TAGAGACAG-TTCTTTGAAACAAA
*
65010 ATTTCA
63 ATTACA
* * * *
65016 TCTCACTTGAGAT-TTTTCTCTTGAAATAAATTTTGTCTCACTTGAGACAGTTTTCTTGAAACAA
1 TCTCACTTGAGATATTTTC-CTTTAAAT--TTTTTGTCTCACTAGAGACAGTTCT-TTGAAAC-A
*
65080 AAATTGCA
61 AAATTACA
65088 TCTCACTTGAGATATTTT
1 TCTCACTTGAGATATTTT
65106 GTCTTGAAAA
Statistics
Matches: 128, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
68 5 0.04
69 32 0.25
70 44 0.34
71 22 0.17
72 21 0.16
73 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (68 bp):
TCTCACTTGAGATATTTTCCTTTAAATTTTTTGTCTCACTAGAGACAGTTCTTTGAAACAAAATT
ACA
Found at i:65047 original size:35 final size:34
Alignment explanation
Indices: 65004--65115 Score: 116
Period size: 35 Copynumber: 3.1 Consensus size: 34
64994 GGTTTCTCTA
65004 AAAAAAATTTCATCTCACTTGAGATTTTTCTCTTG
1 AAAAAAATTTCATCTCACTTGAGATTTTT-TCTTG
* ** **
65039 AAATAAATTTTGTCTCACTTGAGACAGTTTTCTTG
1 AAAAAAATTTCATCTCACTTGAGA-TTTTTTCTTG
*
65074 AAACAAAAATTGCATCTCACTTGAGATATTTTGTCTTG
1 -AA-AAAAATTTCATCTCACTTGAGAT-TTTT-TCTTG
65112 AAAA
1 AAAA
65116 TATCGTCTCA
Statistics
Matches: 61, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
35 26 0.43
36 7 0.11
37 23 0.38
38 5 0.08
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (34 bp):
AAAAAAATTTCATCTCACTTGAGATTTTTTCTTG
Found at i:72908 original size:21 final size:21
Alignment explanation
Indices: 72879--72931 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
72869 ATTCTGACTA
72879 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
72900 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
72921 TCGCAATGCGA
1 TCGCATTGCGA
72932 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:73034 original size:20 final size:20
Alignment explanation
Indices: 72921--73034 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
72911 TTTTCCTAAT
*
72921 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
* ** *
72941 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCG-ATTACGTAAA
* *
72962 TCGTAATGCGATTATGTAAA
1 TCGCAATGCGATTACGTAAA
*
72982 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
73002 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
*
73022 TCGCAATGAGATT
1 TCGCAATGCGATT
73035 CTGACTATCG
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 64 0.82
21 14 0.18
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:73045 original size:40 final size:40
Alignment explanation
Indices: 72921--73048 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
72911 TTTTCCTAAT
* *
72921 TCGCAATGCGAATACGTAAATCGCAACGCGAATT-TGGAAAA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAATTCT-G-AAA
* * *
72962 TCGTAATGCGATTATGTAAATCGCAATGCGAATAC-GTAAA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAATTCTG-AAA
* *
73002 TCGCAATGCGATTACGTAAATCGCAATGAG-ATTCTGACTA
1 TCGCAATGCGATTACGTAAATCGCAATGCGAATTCTGA-AA
73042 TCGCAAT
1 TCGCAAT
73049 ACTGAATTTC
Statistics
Matches: 73, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
39 4 0.05
40 40 0.55
41 29 0.40
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (40 bp):
TCGCAATGCGATTACGTAAATCGCAATGCGAATTCTGAAA
Found at i:73917 original size:24 final size:24
Alignment explanation
Indices: 73890--73943 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
73880 GTATTCGAAA
73890 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
73914 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
73938 TTTGAT
1 TTTGAT
73944 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:76375 original size:20 final size:20
Alignment explanation
Indices: 76350--76443 Score: 95
Period size: 20 Copynumber: 4.7 Consensus size: 20
76340 GACATTCATT
*
76350 TGACTATCTCAACGCGAATA
1 TGACTATCGCAACGCGAATA
76370 TGACTATCGCAACATG-GAA-A
1 TGACTATCGCAAC--GCGAATA
76390 TGACTATCGCAACGCGGAAT-
1 TGACTATCGCAACGC-GAATA
* * *
76410 TGACTATCGCAGCGTGAAAA
1 TGACTATCGCAACGCGAATA
*
76430 TGACTATCGAAACG
1 TGACTATCGCAACG
76444 AGAGAATCGC
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
18 1 0.02
19 3 0.05
20 54 0.87
21 3 0.05
22 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:76405 original size:40 final size:40
Alignment explanation
Indices: 76350--76443 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
76340 GACATTCATT
* *
76350 TGACTATCTCAACGC-GAATATGACTATCGCAACATGGAAA
1 TGACTATCGCAACGCGGAAT-TGACTATCGCAACATGAAAA
* *
76390 TGACTATCGCAACGCGGAATTGACTATCGCAGCGTGAAAA
1 TGACTATCGCAACGCGGAATTGACTATCGCAACATGAAAA
*
76430 TGACTATCGAAACG
1 TGACTATCGCAACG
76444 AGAGAATCGC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 44 0.92
41 4 0.08
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (40 bp):
TGACTATCGCAACGCGGAATTGACTATCGCAACATGAAAA
Found at i:76511 original size:33 final size:34
Alignment explanation
Indices: 76474--76547 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
76464 GAAAATCGTA
** *
76474 TTGCGATTCACTCGTTGCGATTTTCATTT-CGCT
1 TTGCGATTCACTCGTTGCGATAGTCATTTCCGCG
* *
76507 TTGCGATTCTCTCGTTGTGATAGTCATTTCCGCG
1 TTGCGATTCACTCGTTGCGATAGTCATTTCCGCG
76541 TTGCGAT
1 TTGCGAT
76548 AGTCTGTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
33 25 0.71
34 10 0.29
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (34 bp):
TTGCGATTCACTCGTTGCGATAGTCATTTCCGCG
Found at i:76668 original size:14 final size:14
Alignment explanation
Indices: 76649--76685 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
76639 CATCAATTAA
76649 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
76663 ACAAATCATCTTTT
1 ACAAATCAACATTT
76677 ACAAATCAA
1 ACAAATCAA
76686 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:78125 original size:18 final size:20
Alignment explanation
Indices: 78102--78141 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
78092 CTCTTGAGGG
78102 ATGATA-GG-GGCCTCTTGA
1 ATGATAGGGAGGCCTCTTGA
78120 ATGATATGGGAGGCCTCTTGA
1 ATGATA-GGGAGGCCTCTTGA
78141 A
1 A
78142 CGATGACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 2 0.11
21 11 0.58
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGATAGGGAGGCCTCTTGA
Found at i:78654 original size:20 final size:20
Alignment explanation
Indices: 78631--78715 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 20
78621 GAAACTTAAA
78631 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
78651 ATCGCAA--TG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
* **
78665 ATCGCAATGCG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
78684 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
78704 ATCGCAACGCGA
1 ATCGCAACGCGA
78716 TAGTCATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 7 0.13
16 5 0.10
17 4 0.08
18 1 0.02
19 10 0.19
20 25 0.48
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:80652 original size:20 final size:20
Alignment explanation
Indices: 80629--80678 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
80619 CTGAAACTTT
*
80629 AAATTGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
*
80649 AAATCGTAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
**
80669 CTATCGCAAC
1 AAATCGCAAC
80679 GCAAGAATCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:80698 original size:34 final size:33
Alignment explanation
Indices: 80650--80723 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
80640 CGAAAATGAA
* **
80650 AATCGTAACACGAAAATGACTATCGCAACG-CAAG
1 AATCGCAACACG-AAATGAAAATCGCAACGAC-AG
*
80684 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACACGAAATGAAAATCGCAACGACAG
80717 AATCGCA
1 AATCGCA
80724 TTGCGATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 24 0.69
34 11 0.31
ACGTcount: A:0.45, C:0.24, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACACGAAATGAAAATCGCAACGACAG
Found at i:81311 original size:20 final size:20
Alignment explanation
Indices: 81286--81336 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
81276 GCGCTATGTA
81286 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
81306 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
*
81326 ATTCGCATTGC
1 AATCGCATTGC
81337 AAATTAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:81362 original size:21 final size:21
Alignment explanation
Indices: 81338--81380 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
81328 TCGCATTGCA
81338 AATTAGGAAAATCGCAACGCG
1 AATTAGGAAAATCGCAACGCG
* * *
81359 AATTTGGGAAATCGCAATGCG
1 AATTAGGAAAATCGCAACGCG
81380 A
1 A
81381 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.19
Consensus pattern (21 bp):
AATTAGGAAAATCGCAACGCG
Found at i:82459 original size:2 final size:2
Alignment explanation
Indices: 82454--82480 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
82444 AAATATTGTT
82454 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 T
82481 TATTTTAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82696 original size:32 final size:32
Alignment explanation
Indices: 82657--82726 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
82647 AAAGTGTACA
82657 TCATCTTCAATCTCTTACACAAAATACTCCTT
1 TCATCTTCAATCTCTTACACAAAATACTCCTT
* *
82689 TCATCTTCAATCTTTTACACAACATACTCCTT
1 TCATCTTCAATCTCTTACACAAAATACTCCTT
82721 TCATCT
1 TCATCT
82727 AACCAAATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (32 bp):
TCATCTTCAATCTCTTACACAAAATACTCCTT
Found at i:88056 original size:15 final size:15
Alignment explanation
Indices: 88036--88071 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
88026 ACTCAATTTG
88036 AATCGAGTTTTTTCA
1 AATCGAGTTTTTTCA
88051 AATCGAGTTTTTTCA
1 AATCGAGTTTTTTCA
88066 AATCGA
1 AATCGA
88072 ATCGAGTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.42
Consensus pattern (15 bp):
AATCGAGTTTTTTCA
Found at i:94641 original size:31 final size:31
Alignment explanation
Indices: 94606--94684 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
94596 AGTTTCAAAA
*
94606 GTAACAAATTGGTTACTAACATTATCGATTT
1 GTAACAAAATGGTTACTAACATTATCGATTT
* *
94637 GTAACAAAATGGTAACTAACGTTATCGATTT
1 GTAACAAAATGGTTACTAACATTATCGATTT
*
94668 GTAACAAAATAGTTACT
1 GTAACAAAATGGTTACT
94685 CCACTATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (31 bp):
GTAACAAAATGGTTACTAACATTATCGATTT
Found at i:96280 original size:18 final size:18
Alignment explanation
Indices: 96257--96297 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
96247 ACCGGTCACA
96257 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
96275 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
96293 ACCCG
1 ACCCG
96298 TTGACCGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:97619 original size:18 final size:18
Alignment explanation
Indices: 97593--97627 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
97583 TCGAAAGGAC
*
97593 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
97611 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
97628 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:100253 original size:31 final size:31
Alignment explanation
Indices: 100206--100291 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
100196 AACTTACTTG
* * *
100206 TTTAGTACTTAAACTATTAGTTTTGATTCAT
1 TTTAGTACCTAAACTATTAATTTTGATCCAT
* * *
100237 TTTAATACCTAAACTATCAATTTTGATCCGT
1 TTTAGTACCTAAACTATTAATTTTGATCCAT
* *
100268 TTTAGTACCTAAACTTTTATTTTT
1 TTTAGTACCTAAACTATTAATTTT
100292 TTTAAACCGA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (31 bp):
TTTAGTACCTAAACTATTAATTTTGATCCAT
Found at i:100709 original size:2 final size:2
Alignment explanation
Indices: 100696--100734 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
100686 TATTAACGTT
*
100696 TA TA TA TCA TA TA TA -A TA TA TA TA TA TA TA CA TA TA TA T
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
100735 TTAAAATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:100717 original size:16 final size:16
Alignment explanation
Indices: 100696--100734 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
100686 TATTAACGTT
100696 TATATATCATATATA-A
1 TATATAT-ATATATACA
100712 TATATATATATATACA
1 TATATATATATATACA
100728 TATATAT
1 TATATAT
100735 TTAAAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (16 bp):
TATATATATATATACA
Found at i:101405 original size:29 final size:30
Alignment explanation
Indices: 101334--101393 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
101324 CAATTTAAGG
101334 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
101365 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
101394 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:101531 original size:15 final size:15
Alignment explanation
Indices: 101511--101540 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
101501 CCCCCCCCGG
101511 GGGTACAGATACCCC
1 GGGTACAGATACCCC
101526 GGGTACAGATACCCC
1 GGGTACAGATACCCC
101541 CCAGGAGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:101635 original size:20 final size:21
Alignment explanation
Indices: 101595--101637 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
101585 AACAGAATGT
101595 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
101616 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
101637 C
1 C
101638 TGTTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.44, G:0.28, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:101781 original size:20 final size:22
Alignment explanation
Indices: 101743--101782 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
101733 TTTGAGTATA
101743 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
101765 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
101783 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:102036 original size:34 final size:32
Alignment explanation
Indices: 101997--102066 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
101987 TTTTGTAAAG
* *
101997 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
102031 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
102063 GGGA
1 GGGA
102067 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:102950 original size:19 final size:20
Alignment explanation
Indices: 102926--102973 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
102916 AATGATTTTC
*
102926 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
102945 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
102965 TTTTGAAAA
1 TTTTGAAAA
102974 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:104294 original size:29 final size:30
Alignment explanation
Indices: 104223--104282 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
104213 CAATTTAAGG
104223 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
104254 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
104283 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:104398 original size:21 final size:21
Alignment explanation
Indices: 104372--104450 Score: 89
Period size: 21 Copynumber: 4.0 Consensus size: 21
104362 TTCAAGATTG
* *
104372 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATACCCC
104393 CCCAGGGGGTACAGATA---C
1 CCCAGGGGGTACAGATACCCC
104411 CCC---GGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
*
104429 CCCAGGAGGTACAGATACCCC
1 CCCAGGGGGTACAGATACCCC
104450 C
1 C
104451 TGCAGGTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
15 11 0.22
18 8 0.16
21 30 0.61
ACGTcount: A:0.24, C:0.37, G:0.27, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATACCCC
Found at i:104419 original size:15 final size:15
Alignment explanation
Indices: 104399--104428 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
104389 CCCCCCCAGG
104399 GGGTACAGATACCCC
1 GGGTACAGATACCCC
104414 GGGTACAGATACCCC
1 GGGTACAGATACCCC
104429 CCCAGGAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
GGGTACAGATACCCC
Found at i:104429 original size:36 final size:36
Alignment explanation
Indices: 104378--104449 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
104368 ATTGCCCAGG
* * *
104378 GGGTATAGATTCCCCCCCAGGGGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGAGGTACAGATACCCC
104414 GGGTACAGATACCCCCCCAGGAGGTACAGATACCCC
1 GGGTACAGATACCCCCCCAGGAGGTACAGATACCCC
104450 CTGCAGGTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.25, C:0.35, G:0.26, T:0.14
Consensus pattern (36 bp):
GGGTACAGATACCCCCCCAGGAGGTACAGATACCCC
Found at i:104515 original size:22 final size:21
Alignment explanation
Indices: 104484--104548 Score: 121
Period size: 21 Copynumber: 3.0 Consensus size: 21
104474 AACAGAATGT
104484 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
104505 CCAGGGGGGTACCGATTCCCCC
1 CCA-GGGGGTACCGATTCCCCC
104527 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACCGATTCCCCC
104548 C
1 C
104549 TGTTCAACAG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 22 0.51
22 21 0.49
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACCGATTCCCCC
Found at i:104692 original size:20 final size:22
Alignment explanation
Indices: 104654--104693 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
104644 TTTGAGTATA
104654 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
104676 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
104694 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:105874 original size:3 final size:3
Alignment explanation
Indices: 105859--105980 Score: 88
Period size: 3 Copynumber: 40.7 Consensus size: 3
105849 AATAATCTGT
* * *
105859 AGA AGA AGG AGA AGA AGA AGA AGA AGA AGA AAA AGA ATG- AGA AAA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA
* * * * * * * * *
105904 AGA ATA AGA AGA GGT AGTA A-T AGT AGT AGT AGT AGTA A-T AGA AGA
1 AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AG-A AGA AGA AGA
105949 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
105981 TTTCCCTTGA
Statistics
Matches: 97, Mismatches: 16, Indels: 12
0.78 0.13 0.10
Matches are distributed among these distances:
2 3 0.03
3 91 0.94
4 3 0.03
ACGTcount: A:0.60, C:0.00, G:0.31, T:0.09
Consensus pattern (3 bp):
AGA
Found at i:107170 original size:19 final size:19
Alignment explanation
Indices: 107146--107184 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
107136 ATTGCAAAAA
*
107146 TTAAAAGTTAAATTCGAAT
1 TTAAAAGTTAAATTCAAAT
107165 TTAAAAGTTAAATTCAAAT
1 TTAAAAGTTAAATTCAAAT
107184 T
1 T
107185 ACTTACCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (19 bp):
TTAAAAGTTAAATTCAAAT
Found at i:108723 original size:36 final size:38
Alignment explanation
Indices: 108636--108734 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 38
108626 CCCGATTGGG
108636 CTATGTTTTCAAAAAACTATATTATATATGTTTTCAAAAA
1 CTATGTTTTC-AAAAACTATATTATAT-TGTTTTCAAAAA
* *
108676 CCA--TTTT-AAAAATTATATTATATT-TTTTCAAAAA
1 CTATGTTTTCAAAAACTATATTATATTGTTTTCAAAAA
108710 -TATGTTTTCAAAAACTATA-TATATT
1 CTATGTTTTCAAAAACTATATTATATT
108735 ATATAGTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
33 1 0.02
34 10 0.19
35 11 0.21
36 24 0.46
38 4 0.08
40 2 0.04
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (38 bp):
CTATGTTTTCAAAAACTATATTATATTGTTTTCAAAAA
Found at i:108764 original size:73 final size:74
Alignment explanation
Indices: 108637--108774 Score: 167
Period size: 73 Copynumber: 1.9 Consensus size: 74
108627 CCGATTGGGC
*
108637 TATGTTTTCAAAAAACTATATTATATATGTTTTCAAAAACCATTTTAAAAATTAT-AT-TATATT
1 TATGTTTTCAAAAAACTATATTATATATGTTTT-AAAAACCATTATAAAAATTATCATATATATT
108700 TTTTCAAAAA
65 TTTTCAAAAA
* ** *
108710 TATGTTTTC-AAAAACTATATATATTATATAGTTTT-GAAATTATTATAAATATTATCATATATA
1 TATGTTTTCAAAAAACTATAT-TA-TATAT-GTTTTAAAAACCATTATAAAAATTATCATATATA
108773 TT
63 TT
108775 ATATAATGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
72 11 0.20
73 26 0.47
74 7 0.13
75 11 0.20
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.47
Consensus pattern (74 bp):
TATGTTTTCAAAAAACTATATTATATATGTTTTAAAAACCATTATAAAAATTATCATATATATTT
TTTCAAAAA
Found at i:109490 original size:35 final size:35
Alignment explanation
Indices: 109424--109497 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
109414 TTAATAAAAT
* * *
109424 ATGATAAATAAATCTTACCGCAATCAGTTCAAGTG
1 ATGAGAAATAAATCTTACCACAATCAATTCAAGTG
* * *
109459 ATGAGAAATAAATCTTATCATAGTCAATTCAAGTG
1 ATGAGAAATAAATCTTACCACAATCAATTCAAGTG
109494 ATGA
1 ATGA
109498 AATATGAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.30
Consensus pattern (35 bp):
ATGAGAAATAAATCTTACCACAATCAATTCAAGTG
Found at i:119581 original size:18 final size:18
Alignment explanation
Indices: 119558--119600 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
119548 TATGTGGAGG
119558 AAAAATACGATGAATTGA
1 AAAAATACGATGAATTGA
119576 AAAAATACGATGAATTGA
1 AAAAATACGATGAATTGA
119594 AAAAATA
1 AAAAATA
119601 TGAAGAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (18 bp):
AAAAATACGATGAATTGA
Found at i:124048 original size:37 final size:37
Alignment explanation
Indices: 123995--124099 Score: 140
Period size: 37 Copynumber: 2.8 Consensus size: 37
123985 CCTTTTCGTC
*
123995 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
* *
124032 -TCGCTAGGATTCAAACTCCTTAAAATAGGATAGAGTT
1 CT-ACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
* * *
124069 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
124100 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.02
37 56 0.97
38 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
Found at i:124661 original size:22 final size:22
Alignment explanation
Indices: 124568--124661 Score: 63
Period size: 23 Copynumber: 4.3 Consensus size: 22
124558 TTTTTTACAC
*
124568 TATATA-TTATTATTATCTATACA
1 TATATATTTATTATT-T-TATATA
* *
124591 TATAT-TTTTTTA-TTTATTTA
1 TATATATTTATTATTTTATATA
* *
124611 TAT-TCATTTGGTTATTTTTTA-A
1 TATAT-ATTT-ATTATTTTATATA
124633 TACTATATTTATTATTTTATATA
1 TA-TATATTTATTATTTTATATA
124656 TATATA
1 TATATA
124662 CTTTTTTTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
19 1 0.02
20 7 0.13
21 4 0.07
22 20 0.36
23 22 0.40
24 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (22 bp):
TATATATTTATTATTTTATATA
Found at i:124889 original size:18 final size:19
Alignment explanation
Indices: 124863--124898 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
124853 TGTTTTTGGT
*
124863 TTTTTATATTA-TATTATA
1 TTTTCATATTACTATTATA
124881 TTTTCATATTACTATTAT
1 TTTTCATATTACTATTAT
124899 TATTGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTCATATTACTATTATA
Found at i:124942 original size:2 final size:2
Alignment explanation
Indices: 124935--124971 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
124925 TTTACTCATT
124935 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
124972 TTCATTTATT
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:124990 original size:12 final size:13
Alignment explanation
Indices: 124969--125048 Score: 60
Period size: 13 Copynumber: 6.4 Consensus size: 13
124959 TATATATATA
124969 TATTTCATTTATT
1 TATTTCATTTATT
124982 TATTT-ATTTATT
1 TATTTCATTTATT
* *
124994 T-TTCCTTTTATT
1 TATTTCATTTATT
* * *
125006 TTTTTTACTTATT
1 TATTTCATTTATT
*
125019 TTTATTC-TTTATT
1 TAT-TTCATTTATT
125032 T-TTTCATTTATT
1 TATTTCATTTATT
*
125044 CATTT
1 TATTT
125049 TTTCCCTCTG
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.09
12 22 0.42
13 24 0.45
14 2 0.04
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTTCATTTATT
Found at i:125003 original size:16 final size:16
Alignment explanation
Indices: 124984--125033 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
124974 CATTTATTTA
*
124984 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
125000 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
125015 TATT-TTTATTCTTTA-T
1 T-TTATTTATT-TTTACT
125031 TTT
1 TTT
125034 TTCATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 13 0.43
16 13 0.43
17 4 0.13
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:125033 original size:25 final size:24
Alignment explanation
Indices: 124976--125035 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
124966 ATATATTTCA
* * *
124976 TTTATTTATTTATTTATTTTTCCT
1 TTTATTTTTTTACTTATTTTTACT
*
125000 TTTATTTTTTTTACTTATTTTTATT
1 TTTA-TTTTTTTACTTATTTTTACT
125025 CTTTATTTTTT
1 -TTTATTTTTT
125036 CATTTATTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.13
25 22 0.73
26 4 0.13
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTATTTTTTTACTTATTTTTACT
Found at i:127983 original size:19 final size:19
Alignment explanation
Indices: 127959--127995 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
127949 ACCTTACTAA
127959 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
127978 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
127996 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:131450 original size:16 final size:16
Alignment explanation
Indices: 131424--131457 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
131414 AGATCTCATC
131424 AAGAACAAAAAAG-AA
1 AAGAACAAAAAAGCAA
131439 AAGAAGCAAAAAAGCAA
1 AAGAA-CAAAAAAGCAA
131456 AA
1 AA
131458 AAAACAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (16 bp):
AAGAACAAAAAAGCAA
Found at i:132355 original size:22 final size:22
Alignment explanation
Indices: 132281--132357 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
132271 GCTACCCCAT
* *
132281 CAAACCGTTGAGCATTAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
132303 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
132325 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
132347 CAAACCTTTGA
1 CAAACCTTTGA
132358 CCAAACATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:133330 original size:106 final size:106
Alignment explanation
Indices: 133168--134429 Score: 1800
Period size: 106 Copynumber: 12.0 Consensus size: 106
133158 CCACTCAAGG
* * * ** * *
133168 CAACACAAGTTCAACTTCACAATGAAGGGAATGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
133233 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
133274 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAATAATTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
* *
133339 AGCGAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * ** *
133380 CAACGCAAGTTCAACTTCACAACGAAGAGACCGCTGGTTGTCAACAAACGGCTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
*
133445 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
133486 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAAAATTTCCCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
*
133551 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
133592 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
* * *
133657 AGCCAATTTCAACTTCACAGCGAAGGATATTGGTCTCTAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
133698 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
* *
133763 AGCCAATTTCAACTTTACAACGAAGGATATTAGACTCCAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* *
133804 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
* * *
133869 AGCCAATTTCAACTTCACAGCGTAGGATATTGGACTCAAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
133910 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
* *
133975 AGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
134016 CAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTTAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
134081 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
134122 CAACGCAAGTTCTACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
* * *
134187 AGCCAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC-AGA
* * * *** * * *
134228 TAACACAAGCTCAACTTCACGACGAAGGGGTGGCTGATTGTCAA-CAA-AA-TT-TC-A-TTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
* * * * *
134287 AGTCAATTTCAACTTCACAGCGAAAGATATTAGACTCGAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * * * * ** * *
134328 CAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCGGTTCCAA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
** *
134393 AGCCAATTTCAACTTCATGACGGAGGATATTGGACTC
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
134430 AGAACAATGC
Statistics
Matches: 1041, Mismatches: 107, Indels: 16
0.89 0.09 0.01
Matches are distributed among these distances:
100 75 0.07
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 4 0.00
106 948 0.91
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAG
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:135260 original size:37 final size:37
Alignment explanation
Indices: 135158--135262 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
135148 CCTTTTCGTC
*
135158 CTACTAGGATTCAAACTCCTAAAAATAGAATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * * *
135195 TTGCTAGGATTCAAACTCTTTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
135232 CTACTATGATTTAAACTCCTAAAAATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
135263 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:135812 original size:21 final size:21
Alignment explanation
Indices: 135788--135850 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
135778 ATTTGGTTAT
*
135788 TTTTTAATACTATATTTA-TTA
1 TTTTTAATA-TATATATACTTA
*
135809 TTTTTATATATATATATACTTT
1 TTTTTA-ATATATATATACTTA
*
135831 TTTTTAA-ATAT-TTTACTTA
1 TTTTTAATATATATATACTTA
135850 T
1 T
135851 AAGCGTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 7 0.19
20 4 0.11
21 14 0.39
22 11 0.31
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTTAATATATATATACTTA
Found at i:135820 original size:19 final size:19
Alignment explanation
Indices: 135784--135821 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
135774 ATTCATTTGG
135784 TTATTTTTTAATACTATAT
1 TTATTTTTTAATACTATAT
*
135803 TTATTATTTTTATA-TATAT
1 TTATT-TTTTAATACTATAT
135822 ATATACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTTTTAATACTATAT
Found at i:135841 original size:22 final size:21
Alignment explanation
Indices: 135787--135841 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
135777 CATTTGGTTA
*
135787 TTTTTT-AATACTATATTTATT
1 TTTTTTAAATA-TATATATATT
* *
135808 ATTTTTATATATATATATACTT
1 TTTTTTAAATATATATATA-TT
135830 TTTTTTAAATAT
1 TTTTTTAAATAT
135842 TTTACTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTTTAAATATATATATATT
Found at i:136095 original size:2 final size:2
Alignment explanation
Indices: 136088--136124 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
136078 TATTTTACTC
136088 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
136125 TTCATTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:136135 original size:4 final size:4
Alignment explanation
Indices: 136122--136151 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
136112 ATATATATAA
136122 TATT TCATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT T
136152 TTCCTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:138915 original size:20 final size:20
Alignment explanation
Indices: 138892--138929 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
138882 AATGATCACT
138892 TGAATATTCAAATGTTCCCC
1 TGAATATTCAAATGTTCCCC
138912 TGAATATTCAAATGTTCC
1 TGAATATTCAAATGTTCC
138930 AAACACATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (20 bp):
TGAATATTCAAATGTTCCCC
Found at i:142761 original size:2 final size:2
Alignment explanation
Indices: 142754--142779 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
142744 AATCTGTCGT
142754 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
142780 ATCTGAGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.