Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006415.1 Hibiscus syriacus cultivar Beakdansim tig00015474_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: 95801
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3090 original size:12 final size:12
Alignment explanation
Indices: 3071--3102 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3061 TACATATCAT
3071 TCATTATTCTTA
1 TCATTATTCTTA
*
3083 TTATTATTCTTA
1 TCATTATTCTTA
3095 TCATTATT
1 TCATTATT
3103 AGCAACCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.00, T:0.62
Consensus pattern (12 bp):
TCATTATTCTTA
Found at i:3382 original size:23 final size:24
Alignment explanation
Indices: 3344--3390 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
3334 CTAGGGGAAA
*
3344 GTAGAAATTATCCCGAAGGACCAC
1 GTAGAAATTATCCCGAAAGACCAC
3368 GTAGAAA-TATCCCGAAAGACCAC
1 GTAGAAATTATCCCGAAAGACCAC
3391 ATATAACACA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.15
Consensus pattern (24 bp):
GTAGAAATTATCCCGAAAGACCAC
Found at i:3764 original size:6 final size:6
Alignment explanation
Indices: 3755--3807 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
3745 AGATCATCAT
* * *
3755 CATATA CATATG TATA-A CATATA CATATA CATATA CATATCG CATA-A
1 CATATA CATATA CATATA CATATA CATATA CATATA CATAT-A CATATA
3802 CATATA
1 CATATA
3808 ATACATATCA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 7 0.18
6 27 0.71
7 4 0.11
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (6 bp):
CATATA
Found at i:4277 original size:21 final size:22
Alignment explanation
Indices: 4235--4289 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
4225 CGATGTTCCC
4235 TGGTATCGATACCCTCCACATA
1 TGGTATCGATACCCTCCACATA
* *
4257 -GGTATTGATACCTCTTC-CATA
1 TGGTATCGATACC-CTCCACATA
4278 TGGTATCGATAC
1 TGGTATCGATAC
4290 TATTTATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (22 bp):
TGGTATCGATACCCTCCACATA
Found at i:8169 original size:20 final size:22
Alignment explanation
Indices: 8143--8218 Score: 81
Period size: 21 Copynumber: 3.6 Consensus size: 22
8133 CGATGTTCCC
8143 TGGTATCGATACC-C-T-CATA
1 TGGTATCGATACCTCTTCCATA
8162 TAGGTATCGATACCTCTTCCATA
1 T-GGTATCGATACCTCTTCCATA
*
8185 TGGTATCGATA-CTGTT-CATAA
1 TGGTATCGATACCTCTTCCAT-A
*
8206 TTGTATCGATACC
1 TGGTATCGATACC
8219 CCATGCATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.02
20 15 0.31
21 16 0.33
22 12 0.24
23 5 0.10
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (22 bp):
TGGTATCGATACCTCTTCCATA
Found at i:9364 original size:14 final size:15
Alignment explanation
Indices: 9345--9380 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
9335 ATTAATTTTA
*
9345 AAAAAATGTT-ATAT
1 AAAAAATGTTAAAAT
9359 AAAAAATGTTAAAAT
1 AAAAAATGTTAAAAT
9374 AAAAAAT
1 AAAAAAT
9381 AAAATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (15 bp):
AAAAAATGTTAAAAT
Found at i:9435 original size:16 final size:16
Alignment explanation
Indices: 9411--9517 Score: 58
Period size: 16 Copynumber: 6.2 Consensus size: 16
9401 TAAATTTCAT
9411 AAAATAAAA-AAAATA
1 AAAATAAAATAAAATA
***
9426 AAATATAAAA-ATGTTA
1 AAA-ATAAAATAAAATA
*
9442 AAACAGAAAATAATAATA
1 AAA-ATAAAATAA-AATA
9460 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
9476 AAGAAGTGGGAAAATAAAGAT-
1 AA-AA-T---AAAATAAA-ATA
*
9497 AAAACAAAATAAAATTA
1 AAAATAAAATAAAA-TA
9514 AAAA
1 AAAA
9518 AAGAACTGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
15 4 0.06
16 32 0.45
17 15 0.21
18 6 0.08
20 2 0.03
21 10 0.14
22 2 0.03
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:9566 original size:17 final size:18
Alignment explanation
Indices: 9539--9614 Score: 54
Period size: 17 Copynumber: 4.3 Consensus size: 18
9529 AATTTTAAAG
9539 AAAATACAAGG-AAAGATA
1 AAAATACAAGGTAAA-ATA
9557 AAAATA-AAGGTAAAATA
1 AAAATACAAGGTAAAATA
* *
9574 AAAGGTATAA--TAAAAT-
1 AAA-ATACAAGGTAAAATA
* *
9590 AAAATAAAAGATAAAATA
1 AAAATACAAGGTAAAATA
9608 ATAAATA
1 A-AAATA
9615 GTAATAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.08
16 3 0.06
17 22 0.46
18 12 0.25
19 7 0.15
ACGTcount: A:0.70, C:0.01, G:0.11, T:0.18
Consensus pattern (18 bp):
AAAATACAAGGTAAAATA
Found at i:9594 original size:22 final size:22
Alignment explanation
Indices: 9550--9608 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
9540 AAATACAAGG
*
9550 AAAGATAAAAATAAAGGTAAAATA
1 AAAGAT-AAAATAAA-ATAAAATA
* *
9574 AAAGGTATAATAAAATAAAATA
1 AAAGATAAAATAAAATAAAATA
9596 AAAGATAAAATAA
1 AAAGATAAAATAA
9609 TAAATAGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 18 0.60
23 7 0.23
24 5 0.17
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (22 bp):
AAAGATAAAATAAAATAAAATA
Found at i:9606 original size:12 final size:12
Alignment explanation
Indices: 9550--9608 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
9540 AAATACAAGG
9550 AAAGATAAAA-A
1 AAAGATAAAATA
*
9561 TAAAGGTAAAATA
1 -AAAGATAAAATA
* *
9574 AAAGGTATAAT-
1 AAAGATAAAATA
9585 AAA-ATAAAATA
1 AAAGATAAAATA
9596 AAAGATAAAATA
1 AAAGATAAAATA
9608 A
1 A
9609 TAAATAGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 5 0.12
11 6 0.15
12 28 0.70
13 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (12 bp):
AAAGATAAAATA
Found at i:9691 original size:16 final size:17
Alignment explanation
Indices: 9652--9691 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
9642 AGTGTTTCTA
*
9652 AAATAAAAGATAAGAAT
1 AAATAAAAGATAAAAAT
9669 AAATAAAAGA-AAAAAT
1 AAATAAAAGATAAAAAT
*
9685 TAATAAA
1 AAATAAA
9692 TAATCTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
AAATAAAAGATAAAAAT
Found at i:21065 original size:27 final size:26
Alignment explanation
Indices: 21021--21071 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
21011 TAACCTTTTT
21021 ATTTTTTTTATGTTTTTTCATTTACC
1 ATTTTTTTTATGTTTTTTCATTTACC
*
21047 ATTTATTTTTAT-TTATTTTTATTTA
1 ATTT-TTTTTATGTT-TTTTCATTTA
21072 TTTCTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.73
Consensus pattern (26 bp):
ATTTTTTTTATGTTTTTTCATTTACC
Found at i:21079 original size:10 final size:10
Alignment explanation
Indices: 21047--21080 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
21037 TTCATTTACC
21047 ATTTATTTTT
1 ATTTATTTTT
21057 ATTTATTTTT
1 ATTTATTTTT
*
21067 ATTTATTTCT
1 ATTTATTTTT
21077 ATTT
1 ATTT
21081 TACTAACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:31779 original size:105 final size:105
Alignment explanation
Indices: 31331--31777 Score: 804
Period size: 105 Copynumber: 4.3 Consensus size: 105
31321 AGGTTTTACC
* * *
31331 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
31396 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
31436 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
31501 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCGAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
31541 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
31606 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* *
31646 CAGAGCCAATTTCAACTTCGCAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
31711 ACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
31751 CAGAGCCAATTTCAACTTCACGACGAA
1 CAGAGCCAATTTCAACTTCACAACGAA
31778 AGGACCGCTG
Statistics
Matches: 331, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 331 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:31796 original size:62 final size:62
Alignment explanation
Indices: 31699--31839 Score: 273
Period size: 62 Copynumber: 2.3 Consensus size: 62
31689 ACAACGCAAG
31699 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
1 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
31761 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
1 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
*
31823 TTCAACTTCACAACGAA
1 TTCAACTTCACGACGAA
31840 GGATATTGGA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 78 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (62 bp):
TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
Found at i:31797 original size:167 final size:167
Alignment explanation
Indices: 31594--31944 Score: 657
Period size: 167 Copynumber: 2.1 Consensus size: 167
31584 ACAACGCAAG
*
31594 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
*
31659 AACTTCGCAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGC
66 AACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGC
31724 TGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
131 TGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
31761 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
* *
31826 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 AACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGC
31891 TGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
131 TGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
*
31928 TTCAACTTCACAACGAA
1 TTCAACTTCACGACGAA
31945 GGATATTGGG
Statistics
Matches: 179, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
167 179 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (167 bp):
TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
AACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGC
TGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAAT
Found at i:31870 original size:105 final size:105
Alignment explanation
Indices: 31761--31953 Score: 377
Period size: 105 Copynumber: 1.8 Consensus size: 105
31751 CAGAGCCAAT
31761 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
31826 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
31866 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
1 TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
31931 AACTTCACAACGAAGGATATTGG
66 AACTTCACAACGAAGGATATTGG
31954 GCTCGGAACA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 87 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
TTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTC
AACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:34571 original size:19 final size:19
Alignment explanation
Indices: 34544--34582 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
34534 TGTTACACCT
*
34544 AAAATGTTATAAACAATAA
1 AAAAAGTTATAAACAATAA
34563 AAAAAGTTATAAACAATAA
1 AAAAAGTTATAAACAATAA
34582 A
1 A
34583 TATTATTAAT
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:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (19 bp):
AAAAAGTTATAAACAATAA
Found at i:34812 original size:77 final size:75
Alignment explanation
Indices: 34721--35087 Score: 347
Period size: 77 Copynumber: 4.9 Consensus size: 75
34711 AAACCTAAAC
* * *
34721 ATGTCATGGTTCACTAAGAAACAAATTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGGA
1 ATGTCATGGTTCACTAAGAAACAAGTTGCGATATGGAATGTTAATATTTTTATTAATAAAATGG-
34786 TTGATTCCAAGA
65 TTGA-TCCAAGA
* *
34798 ATGTCATGGTTCACTAAGAAACAAGTTGTGATATGGAATTTTAATATTTTTATTAATAAAATAGG
1 ATGTCATGGTTCACTAAGAAACAAGTTGCGATATGGAATGTTAATATTTTTATTAATAAAAT-GG
34863 TTGCA-CCTAAGA
65 TTG-ATCC-AAGA
* * * * * * * *
34875 ATATCATTGTTCACTAATAAATAGGTTACGATCTAGAATGTTAATATTTTTATTAATAAAATGGG
1 ATGTCATGGTTCACTAAGAAACAAGTTGCGATATGGAATGTTAATATTTTTATTAATAAAAT-GG
* *
34940 TTGCGTCCAATA
65 TTG-ATCCAAGA
* * * * *
34952 ATGTCATTGTTCACTAATAAATAGGTTGCGATATGGAATGTTAGTATTTTTATTAATAAAATGGG
1 ATGTCATGGTTCACTAAGAAACAAGTTGCGATATGGAATGTTAATATTTTTATTAATAAAAT-GG
35017 TTG---C--G-
65 TTGATCCAAGA
* * * * * * *
35022 -T-CCATGGTTCACTAATACATAGGTTGTGATATGCAATGTTAATATTTTTATTAATAAAATGAG
1 ATGTCATGGTTCACTAAGAAACAAGTTGCGATATGGAATGTTAATATTTTTATTAATAAAATG-G
35085 TTG
65 TTG
35088 CGTCAAAAAA
Statistics
Matches: 257, Mismatches: 28, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
67 1 0.00
68 57 0.22
69 1 0.00
73 1 0.00
76 2 0.01
77 190 0.74
78 5 0.02
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.38
Consensus pattern (75 bp):
ATGTCATGGTTCACTAAGAAACAAGTTGCGATATGGAATGTTAATATTTTTATTAATAAAATGGT
TGATCCAAGA
Found at i:34899 original size:37 final size:39
Alignment explanation
Indices: 34851--34982 Score: 112
Period size: 37 Copynumber: 3.5 Consensus size: 39
34841 ATATTTTTAT
34851 TAATAAAATAGGTTGC-ACCTAAGAATATCATTGTTCAC
1 TAATAAAATAGGTTGCGACCTAAGAATATCATTGTTCAC
* * * * * * *
34889 TAAT-AAATAGGTTACGATCT-AGAATGTTAATATTTTTAT
1 TAATAAAATAGGTTGCGACCTAAGAAT-ATCAT-TGTTCAC
* * * *
34928 TAATAAAATGGGTTGCGTCC-AATAATGTCATTGTTCAC
1 TAATAAAATAGGTTGCGACCTAAGAATATCATTGTTCAC
34966 TAAT-AAATAGGTTGCGA
1 TAATAAAATAGGTTGCGA
34983 TATGGAATGT
Statistics
Matches: 70, Mismatches: 19, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
37 26 0.37
38 18 0.26
39 11 0.16
40 15 0.21
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (39 bp):
TAATAAAATAGGTTGCGACCTAAGAATATCATTGTTCAC
Found at i:35021 original size:40 final size:38
Alignment explanation
Indices: 34910--35023 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 38
34900 TTACGATCTA
34910 GAATGTTAATATTTTTATTAATAAAATGGGTTGCGTCCAAT
1 GAATGTT-ATATTTTTATTAATAAAATGGGTTGCGT-C-AT
* * * * *
34951 -AATGTCAT-TGTTCACTAAT-AAATAGGTTGCGAT-AT
1 GAATGTTATATTTTTATTAATAAAATGGGTTGCG-TCAT
34986 GGAATGTTAGTATTTTTATTAATAAAATGGGTTGCGTC
1 -GAATGTTA-TATTTTTATTAATAAAATGGGTTGCGTC
35024 CATGGTTCAC
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
35 2 0.04
37 17 0.30
38 10 0.18
39 11 0.20
40 16 0.29
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (38 bp):
GAATGTTATATTTTTATTAATAAAATGGGTTGCGTCAT
Found at i:35069 original size:68 final size:68
Alignment explanation
Indices: 34960--35091 Score: 219
Period size: 68 Copynumber: 1.9 Consensus size: 68
34950 TAATGTCATT
* * *
34960 GTTCACTAATAAATAGGTTGCGATATGGAATGTTAGTATTTTTATTAATAAAATGGGTTGCGTCC
1 GTTCACTAATAAATAGGTTGCGATATGCAATGTTAATATTTTTATTAATAAAATGAGTTGCGTCC
35025 ATG
66 ATG
* *
35028 GTTCACTAATACATAGGTTGTGATATGCAATGTTAATATTTTTATTAATAAAATGAGTTGCGTC
1 GTTCACTAATAAATAGGTTGCGATATGCAATGTTAATATTTTTATTAATAAAATGAGTTGCGTC
35092 AAAAAATATT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (68 bp):
GTTCACTAATAAATAGGTTGCGATATGCAATGTTAATATTTTTATTAATAAAATGAGTTGCGTCC
ATG
Found at i:35156 original size:145 final size:145
Alignment explanation
Indices: 34883--35157 Score: 322
Period size: 145 Copynumber: 1.9 Consensus size: 145
34873 GAATATCATT
* * *
34883 GTTCACTAATAAATAGGTTACGATCTAGAATGTTAATATTTTTATTAATAAAATGGGTTGCGTCC
1 GTTCACTAATAAATAGGTTACGATATAGAATGTTAATATTTTTATTAATAAAATGAGTTGCGTCA
* * * * * * * ** *
34948 AATAATGTCATTGTTCACTAATAAATAGGTTGCGATATGGAATGTTAGTATTTTTATTAATAAAA
66 AAAAATATCATAGTTCACTAAGAAACAAGTTGCGATATGAAATAATAATATTTTTATTAATAAAA
35013 TGGGTTGCGTCCATG
131 TGGGTTGCGTCCATG
* **
35028 GTTCACTAATACATAGGTTGTGATAT-GCAATGTTAATATTTTTATTAATAAAATGAGTTGCGTC
1 GTTCACTAATAAATAGGTTACGATATAG-AATGTTAATATTTTTATTAATAAAATGAGTTGCGTC
* * * *
35092 AAAAAATATTATAGTTTACTAAGAAAGCAAGTTGTGATCTGAAATAATAAT-TTTTCTATT-ATA
65 AAAAAATATCATAGTTCACTAAGAAA-CAAGTTGCGATATGAAATAATAATATTTT-TATTAATA
35155 AAA
128 AAA
35158 AATTCGAAAG
Statistics
Matches: 107, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
144 1 0.01
145 86 0.80
146 20 0.19
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (145 bp):
GTTCACTAATAAATAGGTTACGATATAGAATGTTAATATTTTTATTAATAAAATGAGTTGCGTCA
AAAAATATCATAGTTCACTAAGAAACAAGTTGCGATATGAAATAATAATATTTTTATTAATAAAA
TGGGTTGCGTCCATG
Found at i:35269 original size:20 final size:20
Alignment explanation
Indices: 35240--35277 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35230 AGAATGCCGT
*
35240 AAAGTGTTGATACTTTTATA
1 AAAGTATTGATACTTTTATA
35260 AAAGTATTGATACTTTTA
1 AAAGTATTGATACTTTTA
35278 AATTTGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (20 bp):
AAAGTATTGATACTTTTATA
Found at i:35343 original size:135 final size:135
Alignment explanation
Indices: 35191--35442 Score: 346
Period size: 135 Copynumber: 1.9 Consensus size: 135
35181 TTTTCAAAAA
* * * *
35191 TATCGATACTTTCGAATTTAAAGAAAAACATGGA-AAATGAGAATGCCGTAAAGTGTTGATACTT
1 TATCGATACTTTCGAATTTAAAGAAAAACAT-GACAAATGAGAA-GCCGCAAAATATCGATACTT
* * * * *
35255 TTATAAAAGTATTGATACTTTTAAATTTGAAA-TTTAAAATATCATTTTCTATTTTTTTTAAAAT
64 TTACAAAAATATCGATACTTTTAAATTTGAAAGTTCAAAATATCATGTTCTATTTTTTTTAAAAT
35319 TTGACAG
129 TTGACAG
* * *
35326 TATCGATACTTTTGAATTTAAAGAAAAACATGACAAATGAGAAGCTGCAAAATATCGATTCTTTT
1 TATCGATACTTTCGAATTTAAAGAAAAACATGACAAATGAGAAGCCGCAAAATATCGATACTTTT
* *
35391 CCAAAAATATCGATACTTTTAAATTTGAAAGTTCAATATATCATGTTCTATT
66 ACAAAAATATCGATACTTTTAAATTTGAAAGTTCAAAATATCATGTTCTATT
35443 CAATTTTTTT
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 44 0.44
135 57 0.56
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (135 bp):
TATCGATACTTTCGAATTTAAAGAAAAACATGACAAATGAGAAGCCGCAAAATATCGATACTTTT
ACAAAAATATCGATACTTTTAAATTTGAAAGTTCAAAATATCATGTTCTATTTTTTTTAAAATTT
GACAG
Found at i:36411 original size:77 final size:77
Alignment explanation
Indices: 36285--36573 Score: 273
Period size: 77 Copynumber: 3.7 Consensus size: 77
36275 TCTTGTGGGC
* * *
36285 AATCCATTTTATTAAT-AAAATATTAACATTCCAGACCACAATTTATTTCTTAGTGAACTATGAT
1 AATCCATTTTATTAATAAAAATATTAACATTCCAGATCACAACTTATTTCTTAGTGAACAATGAT
* *
36349 ATCCTTGAGCGA
66 ATTCTTGGGCGA
* * *** *
36361 AATCCATTTTATTAATAAAAATATTAACATTTCATATTGTAACTTATTTCTTAGTGAAAAATGAT
1 AATCCATTTTATTAATAAAAATATTAACATTCCAGATCACAACTTATTTCTTAGTGAACAATGAT
*
36426 ATTCTTGGGTGCA
66 ATTCTTGGGCG-A
* * * * *
36439 ACAT--ATTTTATTAA-AAAAGTATTAACATTACATTACAAATAACAACCTATTTCTTAATGAAC
1 A-ATCCATTTTATTAATAAAAATATTAACATT-C----CAGATCACAACTTATTTCTTAGTGAAC
* *
36501 AATGACATTCTTGGGCGT
60 AATGATATTCTTGGGCGA
** *
36519 AA-CTCATTTTATTAATAAAAATATTAACATTCCAGATCGTAACATATTTCTTAGT
1 AATC-CATTTTATTAATAAAAATATTAACATTCCAGATCACAACTTATTTCTTAGT
36574 AAATCGTGAA
Statistics
Matches: 170, Mismatches: 31, Indels: 23
0.76 0.14 0.10
Matches are distributed among these distances:
76 30 0.18
77 74 0.44
78 2 0.01
79 3 0.02
80 1 0.01
81 46 0.27
82 14 0.08
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (77 bp):
AATCCATTTTATTAATAAAAATATTAACATTCCAGATCACAACTTATTTCTTAGTGAACAATGAT
ATTCTTGGGCGA
Found at i:38738 original size:2 final size:2
Alignment explanation
Indices: 38731--38772 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
38721 AAATAAAGTA
38731 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
38773 TTGTATACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39009 original size:21 final size:21
Alignment explanation
Indices: 38985--39024 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38975 ATATATATAT
*
38985 ATATTTGTTT-TTATAAATACA
1 ATATTTATTTATT-TAAATACA
39006 ATATTTATTTATTTAAATA
1 ATATTTATTTATTTAAATA
39025 TTTTTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
ATATTTATTTATTTAAATACA
Found at i:40740 original size:3 final size:3
Alignment explanation
Indices: 40723--40792 Score: 72
Period size: 3 Copynumber: 23.0 Consensus size: 3
40713 ACATGTAATT
* *
40723 TAA TAA -AA TTAA TAA TAA TAA TAA TAAA TAA TAA TAT TAA TAT TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
*
40769 TTAT TAA TAA TAA TAA -AA TAA TAA
1 -TAA TAA TAA TAA TAA TAA TAA TAA
40793 AAACGAATAG
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 4 0.07
3 45 0.80
4 7 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:40752 original size:25 final size:25
Alignment explanation
Indices: 40724--40792 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
40714 CATGTAATTT
40724 AATAA-AATTAATAATAATAATAATA
1 AATAATAA-TAATAATAATAATAATA
* * * *
40749 AATAATAATATTAATATTAATTATT
1 AATAATAATAATAATAATAATAATA
40774 AATAATAATAA-AATAATAA
1 AATAATAATAATAATAATAA
40793 AAACGAATAG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 7 0.19
25 28 0.76
26 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATAATAATAATAATAATAATAATA
Found at i:40755 original size:28 final size:28
Alignment explanation
Indices: 40723--40792 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
40713 ACATGTAATT
40723 TAATAAAATTAATAATAA-TAATAATAAA
1 TAATAAAATTAATAATAATTAATAAT-AA
* * *
40751 TAATAATATTAATATTAATTATTAATAA
1 TAATAAAATTAATAATAATTAATAATAA
40779 TAATAAAA-TAATAA
1 TAATAAAATTAATAA
40793 AAACGAATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.14
28 25 0.69
29 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
TAATAAAATTAATAATAATTAATAATAA
Found at i:42389 original size:22 final size:22
Alignment explanation
Indices: 42289--42387 Score: 146
Period size: 22 Copynumber: 4.5 Consensus size: 22
42279 AATAAAGTTT
*
42289 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
42311 TCATCTTTGAAAAGGGAATAC-A
1 TCATCTTTGAAAAGAGAAT-CTA
*
42333 TCATCTTTGAAAAGAGAATCTT
1 TCATCTTTGAAAAGAGAATCTA
*
42355 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
42377 TCATCTTTGAA
1 TCATCTTTGAA
42388 GAAATATTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
21 1 0.01
22 67 0.97
23 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:48628 original size:35 final size:34
Alignment explanation
Indices: 48569--48638 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 34
48559 GGAAAGATGC
*
48569 AAATGCAAAAATGAAAATGTAAATACAAACGTAA
1 AAATGCAAAAATGAAAATGCAAATACAAACGTAA
*
48603 AAATGCAAAAATGCAAAATGCAAATACAAATGTAA
1 AAATGCAAAAATG-AAAATGCAAATACAAACGTAA
48638 A
1 A
48639 TATGTGAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 13 0.39
35 20 0.61
ACGTcount: A:0.61, C:0.10, G:0.11, T:0.17
Consensus pattern (34 bp):
AAATGCAAAAATGAAAATGCAAATACAAACGTAA
Found at i:50145 original size:17 final size:18
Alignment explanation
Indices: 50114--50148 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
50104 TAATATCTAA
50114 AAAGGATATAAAAATAAT
1 AAAGGATATAAAAATAAT
50132 AAAGGATA-AAAAATAAT
1 AAAGGATATAAAAATAAT
50149 TGAAAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (18 bp):
AAAGGATATAAAAATAAT
Found at i:51212 original size:2 final size:2
Alignment explanation
Indices: 51205--51231 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51195 CTAGAATAAC
51205 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
51232 TTGTTTTTAT
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:51253 original size:21 final size:21
Alignment explanation
Indices: 51228--51267 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51218 ATATATATAT
*
51228 ATATTTGTTT-TTATAAATACA
1 ATATTTATTTATT-TAAATACA
51249 ATATTTATTTATTTAAATA
1 ATATTTATTTATTTAAATA
51268 TATTTTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
ATATTTATTTATTTAAATACA
Found at i:52034 original size:3 final size:3
Alignment explanation
Indices: 52001--52054 Score: 51
Period size: 3 Copynumber: 18.0 Consensus size: 3
51991 AAATGACCTG
*
52001 TAA T-A TAA TAA -AA TTAA TAT TAA TAAA TAA TAA TAA TTAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA T-AA TAA TAA TAA -TAA TAA TAA
52047 -AA TAA TAA
1 TAA TAA TAA
52055 AAACGAATGG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 6 0.14
3 29 0.67
4 8 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:52034 original size:10 final size:10
Alignment explanation
Indices: 52001--52054 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
51991 AAATGACCTG
52001 TAATATAATAA
1 TAATA-AATAA
* *
52012 -AATTAATAT
1 TAATAAATAA
52021 TAATAAATAA
1 TAATAAATAA
*
52031 TAATAATTAA
1 TAATAAATAA
52041 TAATAAAATAA
1 TAAT-AAATAA
52052 TAA
1 TAA
52055 AAACGAATGG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 4 0.11
10 23 0.66
11 8 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAATAAATAA
Found at i:52037 original size:13 final size:13
Alignment explanation
Indices: 52005--52051 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
51995 GACCTGTAAT
*
52005 ATAATAA-AATTA
1 ATAATAATAAATA
*
52017 ATATTAATAAATA
1 ATAATAATAAATA
*
52030 ATAATAATTAATA
1 ATAATAATAAATA
52043 ATAA-AATAA
1 ATAATAATAA
52052 TAAAAACGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATAATAAATA
Found at i:53093 original size:13 final size:13
Alignment explanation
Indices: 53075--53099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53065 AATTAAAAAG
53075 AGAGAGAGAAACT
1 AGAGAGAGAAACT
53088 AGAGAGAGAAAC
1 AGAGAGAGAAAC
53100 AAACGTAGCT
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:0.56, C:0.08, G:0.32, T:0.04
Consensus pattern (13 bp):
AGAGAGAGAAACT
Found at i:54635 original size:31 final size:31
Alignment explanation
Indices: 54597--54704 Score: 118
Period size: 31 Copynumber: 3.5 Consensus size: 31
54587 CGAGCCATAT
*
54597 ACGAGCCATACGAGCAAATGGGGAGCATGCA
1 ACGAGCCATACGAGCCAATGGGGAGCATGCA
54628 ACGAGCCATACGAGCCAAT-GGGAGCATGC-
1 ACGAGCCATACGAGCCAATGGGGAGCATGCA
* *
54657 A-G-G-AATAGAGAGCCAATGGGGAGCATGCA
1 ACGAGCCATA-CGAGCCAATGGGGAGCATGCA
*
54686 ATGAGCCATATACGAGCCA
1 ACGAGCC--ATACGAGCCA
54705 TACGAGTCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
26 3 0.05
27 9 0.14
28 11 0.17
29 2 0.03
30 11 0.17
31 19 0.30
33 6 0.09
34 3 0.05
ACGTcount: A:0.35, C:0.22, G:0.31, T:0.11
Consensus pattern (31 bp):
ACGAGCCATACGAGCCAATGGGGAGCATGCA
Found at i:54787 original size:29 final size:29
Alignment explanation
Indices: 54737--54814 Score: 122
Period size: 29 Copynumber: 2.7 Consensus size: 29
54727 AGGAATAGAG
* *
54737 AGGTCGCCATGCAG-CCTAGGCGACCTTGT
1 AGGTCGCCATGTAGTCC-CGGCGACCTTGT
54766 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
54795 AGGTCGCCATGTAGTCCCGG
1 AGGTCGCCATGTAGTCCCGG
54815 TGCCATTCCC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 44 0.96
30 2 0.04
ACGTcount: A:0.15, C:0.31, G:0.32, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:54923 original size:27 final size:27
Alignment explanation
Indices: 54891--54943 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
54881 CCTACAGCTC
54891 CCAATGCATGCATGTGAACCATTTGAG
1 CCAATGCATGCATGTGAACCATTTGAG
54918 CCAATGCATGCATGTGAACCATTTGA
1 CCAATGCATGCATGTGAACCATTTGA
54944 TTATTGGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (27 bp):
CCAATGCATGCATGTGAACCATTTGAG
Found at i:55083 original size:23 final size:23
Alignment explanation
Indices: 55055--55100 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
55045 AAAAGAAAGA
*
55055 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGAATGCAG
55078 AAGAAAGGGAGAAGAGAATGCAG
1 AAGAAAGGGAGAAGAGAATGCAG
55101 CCGAGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.39, T:0.07
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGAATGCAG
Found at i:55129 original size:21 final size:21
Alignment explanation
Indices: 55105--55157 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
55095 ATGCAGCCGA
55105 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
55126 GAAAGAAAGAAAGGGAGAAAG
1 GAAAGAAAGAAAGGGAGAAAG
*
55147 GAAAGTAAGAA
1 GAAAGAAAGAA
55158 GAAGAAAGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (21 bp):
GAAAGAAAGAAAGGGAGAAAG
Found at i:55151 original size:17 final size:16
Alignment explanation
Indices: 55103--55134 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
55093 GAATGCAGCC
55103 GAGAAAGAAAGAAAGG
1 GAGAAAGAAAGAAAGG
55119 GAGAAAGGAAAGAAAG
1 GAGAAA-GAAAGAAAG
55135 AAAGGGAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAAAGAAAGAAAGG
Found at i:55421 original size:44 final size:46
Alignment explanation
Indices: 55358--55448 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 46
55348 GTTATATAGT
*
55358 TAAAAAATAATTAATTAGTTTGT-TTTGTT-AATAGTT-AGTTATA
1 TAAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
*
55401 TAAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
1 TAAAAAA-TAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
55448 T
1 T
55449 TTGATTGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 7 0.17
44 15 0.36
45 5 0.12
46 7 0.17
47 8 0.19
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (46 bp):
TAAAAAATAATTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATA
Found at i:55525 original size:32 final size:34
Alignment explanation
Indices: 55489--55566 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 34
55479 TTAGTTAGTA
*
55489 AGTTTATTAGTAG-TATA-TTATAATGAAAA-AAT
1 AGTTTATTAGTAGTTATAGTTAT-ATAAAAAGAAT
*
55521 AGTTTATTAGTTAGTTTTAGTTATATAAAAAGAAT
1 AGTTTATTAG-TAGTTATAGTTATATAAAAAGAAT
*
55556 ATTTTATTAGT
1 AGTTTATTAGT
55567 TGTTTAAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 10 0.26
33 3 0.08
34 10 0.26
35 16 0.41
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (34 bp):
AGTTTATTAGTAGTTATAGTTATATAAAAAGAAT
Found at i:55644 original size:16 final size:16
Alignment explanation
Indices: 55612--55658 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
55602 TTTAAAAAGT
*
55612 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
55628 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
55644 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
55659 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:55653 original size:15 final size:14
Alignment explanation
Indices: 55633--55663 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
55623 GTTTATTAGT
55633 TTATTATATTATAAG
1 TTATTATATTA-AAG
55648 TTATTATATTAAAG
1 TTATTATATTAAAG
55662 TT
1 TT
55664 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:57839 original size:17 final size:17
Alignment explanation
Indices: 57817--57849 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57807 CAATGATTTT
*
57817 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
57834 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
57850 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:57887 original size:25 final size:24
Alignment explanation
Indices: 57824--57888 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
57814 TTTTAGTATC
* *
57824 AAATCATTACTAGTATCAAATAATT
1 AAATCATTAATA-AATCAAATAATT
* *
57849 AAAT-ATTTAGTAAATCAAATATTTT
1 AAATCA-TTAATAAATCAAATA-ATT
57874 AAATCATTAATAAAT
1 AAATCATTAATAAAT
57889 TTGACTATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 9 0.27
25 23 0.70
26 1 0.03
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (24 bp):
AAATCATTAATAAATCAAATAATT
Found at i:58031 original size:35 final size:37
Alignment explanation
Indices: 57950--58036 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
57940 TTAGTATTCT
* * *
57950 ATAATTATTAGT-AATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAAATAATTACTAAATCAATAG-ACTAA
*
57988 ATCATTATTATAAATAATTACTAAAT-AATA-ACTAA
1 ATAATTATTATAAATAATTACTAAATCAATAGACTAA
58023 ATAATTATTATAAA
1 ATAATTATTATAAA
58037 ATCATTATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (37 bp):
ATAATTATTATAAATAATTACTAAATCAATAGACTAA
Found at i:58057 original size:12 final size:13
Alignment explanation
Indices: 57966--58193 Score: 120
Period size: 14 Copynumber: 17.1 Consensus size: 13
57956 ATTAGTAATA
57966 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
57980 AGTATTAAATCATT
1 ATTA-TAAATCATT
57994 ATTATAAAT-A--
1 ATTATAAATCATT
58004 ATTACTAAAT-A--
1 ATTA-TAAATCATT
* *
58015 ATAACTAAATAATT
1 ATTA-TAAATCATT
58029 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
58043 ATTAT-AATGATT
1 ATTATAAATCATT
58055 ATTATCAAATCATT
1 ATTAT-AAATCATT
58069 ACTAAATCATCAAATCATT
1 A-T---T-AT-AAATCATT
*
58088 AAATATTTAAATCATT
1 --AT-TATAAATCATT
58104 A-T-TAAATCATT
1 ATTATAAATCATT
* *
58115 TTTAT-AATGATT
1 ATTATAAATCATT
58127 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
58141 ATTAT-AATGATT
1 ATTATAAATCATT
58153 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
58167 ACTAT-AATGATT
1 ATTATAAATCATT
58179 ATTATCAAATCATT
1 ATTAT-AAATCATT
58193 A
1 A
58194 CTAAATCATC
Statistics
Matches: 174, Mismatches: 18, Indels: 44
0.74 0.08 0.19
Matches are distributed among these distances:
10 4 0.02
11 24 0.14
12 45 0.26
13 9 0.05
14 66 0.38
15 1 0.01
16 8 0.05
17 1 0.01
18 3 0.02
19 11 0.06
20 1 0.01
21 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:58064 original size:26 final size:26
Alignment explanation
Indices: 57966--58193 Score: 174
Period size: 26 Copynumber: 9.2 Consensus size: 26
57956 ATTAGTAATA
* * *
57966 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
57991 ATTATTATAA--ATAATTA-CTAAATA
1 ATTATTATAATGATTATTATC-AAATC
* * * *
58015 ATAACTA-AATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
58040 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
58066 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
58089 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
*
58112 ATTTTTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
58138 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
58164 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
58190 ATTA
1 ATTA
58194 CTAAATCATC
Statistics
Matches: 158, Mismatches: 31, Indels: 27
0.73 0.14 0.12
Matches are distributed among these distances:
21 4 0.03
22 2 0.01
23 16 0.10
24 20 0.13
25 28 0.18
26 87 0.55
27 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:58190 original size:124 final size:123
Alignment explanation
Indices: 57982--58251 Score: 445
Period size: 124 Copynumber: 2.2 Consensus size: 123
57972 AAATCATTAG
* * *
57982 TATTAAATCATTATTATAA--ATAATTACTAAATAATAACTAAATAATTATTATAAAATCATTAT
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCATTAC
58045 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* * * * *
58103 TATTAAATCATTTTTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTA-AATAATTATTATAAAATCATTA
58168 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
65 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
58227 TATTAAATCATTTTTATAATGATTA
1 TATTAAATCATTTTTATAATGATTA
58252 ATAAATACAT
Statistics
Matches: 138, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
121 18 0.13
123 17 0.12
124 103 0.75
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (123 bp):
TATTAAATCATTTTTATAATGATTATTACTAAATAATAACTAAATAATTATTATAAAATCATTAC
TATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:60377 original size:26 final size:24
Alignment explanation
Indices: 60319--60377 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
60309 CTAATAAACC
*
60319 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
60343 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
60371 TAATAAT
1 TAATAAT
60378 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:61227 original size:28 final size:30
Alignment explanation
Indices: 61187--61249 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
61177 ATTTTTTATA
*
61187 TAATATAATATATAACTTAAACTAATAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
61217 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
61245 TAATA
1 TAATA
61250 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:61256 original size:28 final size:28
Alignment explanation
Indices: 61191--61256 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
61181 TTTATATAAT
*
61191 ATAATATATAACTTAAACTAATAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
61219 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
61247 ATAATTTATA
1 ATAATATATA
61257 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:61259 original size:21 final size:21
Alignment explanation
Indices: 61226--61274 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
61216 CTAATATAAT
61226 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
61247 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
61268 ATTAACT
1 A-TAACT
61275 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:61777 original size:25 final size:25
Alignment explanation
Indices: 61749--61822 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
61739 ACACCGTTCG
61749 ACGTGCATGGCCATGCACAGTTCCC
1 ACGTGCATGGCCATGCACAGTTCCC
* *
61774 ACGT-C----CCATGCACAGCAT-GC
1 ACGTGCATGGCCATGCACAG-TTCCC
61794 ATC-TGCATGGCCATGCACAGTTCCC
1 A-CGTGCATGGCCATGCACAGTTCCC
61819 ACGT
1 ACGT
61823 CCCATGCACA
Statistics
Matches: 36, Mismatches: 4, Indels: 18
0.62 0.07 0.31
Matches are distributed among these distances:
20 13 0.36
21 3 0.08
24 3 0.08
25 17 0.47
ACGTcount: A:0.22, C:0.36, G:0.22, T:0.20
Consensus pattern (25 bp):
ACGTGCATGGCCATGCACAGTTCCC
Found at i:61784 original size:20 final size:20
Alignment explanation
Indices: 61759--61833 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
61749 ACGTGCATGG
61759 CCATGCACAGTTCCCACGTC
1 CCATGCACAGTTCCCACGTC
* * *
61779 CCATGCACAGCAT-GCATCTGCATGG
1 CCATGCACAG-TTCCCA-C-G--T-C
61804 CCATGCACAGTTCCCACGTC
1 CCATGCACAGTTCCCACGTC
61824 CCATGCACAG
1 CCATGCACAG
61834 CATGCATCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
20 22 0.52
21 3 0.07
22 1 0.02
23 1 0.02
24 3 0.07
25 12 0.29
ACGTcount: A:0.23, C:0.40, G:0.19, T:0.19
Consensus pattern (20 bp):
CCATGCACAGTTCCCACGTC
Found at i:61802 original size:45 final size:45
Alignment explanation
Indices: 61752--61841 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
61742 CCGTTCGACG
61752 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
1 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
61797 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
1 TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
61842 CCCTCCCCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (45 bp):
TGCATGGCCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC
Found at i:61843 original size:25 final size:25
Alignment explanation
Indices: 61770--61843 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
61760 CATGCACAGT
61770 TCCCACGTCCCATGCACAGCATGCA
1 TCCCACGTCCCATGCACAGCATGCA
* * *
61795 TCTGCATG-GCCATGCACAG--T---
1 TC-CCACGTCCCATGCACAGCATGCA
61815 TCCCACGTCCCATGCACAGCATGCA
1 TCCCACGTCCCATGCACAGCATGCA
61840 TCCC
1 TCCC
61844 CTCCCCCATG
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.08
20 12 0.33
22 1 0.03
23 1 0.03
25 16 0.44
26 3 0.08
ACGTcount: A:0.22, C:0.42, G:0.18, T:0.19
Consensus pattern (25 bp):
TCCCACGTCCCATGCACAGCATGCA
Found at i:61853 original size:45 final size:45
Alignment explanation
Indices: 61759--61870 Score: 142
Period size: 45 Copynumber: 2.6 Consensus size: 45
61749 ACGTGCATGG
* **
61759 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCTGCATGG
1 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCTCCATCC
*
61804 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATC-CCCTCCC
1 CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCTCCAT-CC
*
61849 CCATG--CA-TTCCCACGGCCCATG
1 CCATGCACAGTTCCCACGTCCCATG
61871 TTGATTTTTG
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
42 14 0.23
43 2 0.03
44 2 0.03
45 43 0.70
ACGTcount: A:0.21, C:0.44, G:0.17, T:0.19
Consensus pattern (45 bp):
CCATGCACAGTTCCCACGTCCCATGCACAGCATGCATCTCCATCC
Found at i:66537 original size:2 final size:2
Alignment explanation
Indices: 66530--66593 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
66520 AGAAATATGA
66530 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
66572 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
66594 CATCATTTAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75222 original size:4 final size:4
Alignment explanation
Indices: 75213--75269 Score: 53
Period size: 4 Copynumber: 13.8 Consensus size: 4
75203 ATCAAAATGA
* * *
75213 AAAT AAAT -AAT AAAT AAAT GAAAT AAAAA AAAT AAAA AAAT AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT AAAT
75262 AAAAT AAA
1 -AAAT AAA
75270 AAGAAATATA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
3 3 0.07
4 29 0.67
5 11 0.26
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:75246 original size:25 final size:25
Alignment explanation
Indices: 75206--75284 Score: 72
Period size: 25 Copynumber: 3.1 Consensus size: 25
75196 GACCTAAATC
* *
75206 AAAATGAAAATAAAT-AATAAATAAA
1 AAAAT-AAAAAAAATAAAAAAATAAA
*
75231 TGAAATAAAAAAAATAAAAAAATAAA
1 -AAAATAAAAAAAATAAAAAAATAAA
* *
75257 AAAATAAAATAAAA-AGAAATATAAA
1 AAAATAAAA-AAAATAAAAAAATAAA
75282 AAA
1 AAA
75285 TATATATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
25 28 0.62
26 17 0.38
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAATAAAAAAAATAAAAAAATAAA
Found at i:75267 original size:30 final size:30
Alignment explanation
Indices: 75212--75286 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
75202 AATCAAAATG
* * *
75212 AAAAT-AAATAATAAATAAATGAAATAAAA
1 AAAATAAAAAAATAAAAAAATAAAATAAAA
75241 AAAATAAAAAAATAAAAAAATAAAATAAAA
1 AAAATAAAAAAATAAAAAAATAAAATAAAA
75271 AGAAATATAAAAAATA
1 A-AAATA-AAAAAATA
75287 TATATTAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.12
30 22 0.55
31 5 0.12
32 8 0.20
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (30 bp):
AAAATAAAAAAATAAAAAAATAAAATAAAA
Found at i:75288 original size:9 final size:8
Alignment explanation
Indices: 75206--75286 Score: 67
Period size: 8 Copynumber: 9.8 Consensus size: 8
75196 GACCTAAATC
75206 AAAATGAAA
1 AAAAT-AAA
75215 ATAAAT-AA
1 A-AAATAAA
*
75223 TAAATAAA
1 AAAATAAA
*
75231 TGAAATAAAA
1 -AAAAT-AAA
75241 AAAATAAA
1 AAAATAAA
75249 AAAATAAA
1 AAAATAAA
75257 AAAATAAA
1 AAAATAAA
*
75265 ATAA-AAA
1 AAAATAAA
*
75272 GAAATATAA
1 AAAATA-AA
75281 AAAATA
1 AAAATA
75287 TATATTAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
7 9 0.15
8 27 0.46
9 16 0.27
10 7 0.12
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (8 bp):
AAAATAAA
Found at i:75418 original size:16 final size:16
Alignment explanation
Indices: 75397--75427 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
75387 ACCATATATT
*
75397 ATATGTTTTTAAAAAA
1 ATATGTTTTCAAAAAA
75413 ATATGTTTTCAAAAA
1 ATATGTTTTCAAAAA
75428 CTATAATATA
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:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (16 bp):
ATATGTTTTCAAAAAA
Found at i:75451 original size:38 final size:38
Alignment explanation
Indices: 75367--75502 Score: 143
Period size: 38 Copynumber: 3.6 Consensus size: 38
75357 AGTATATACA
* * *
75367 TTTCCAAAA-ATGTTTT-TAAAACCATATATTATATGTT
1 TTTCAAAAATATGTTTTCAAAAACTATATATTATATG-T
*
75404 TTTAAAAAAATATGTTTTCAAAAACTATA-ATATATATGT
1 TTT-CAAAAATATGTTTTCAAAAACTATATAT-TATATGT
* * *
75443 TTTCAAAAACACGTTTTCAAAAACTATATATTATACGT
1 TTTCAAAAATATGTTTTCAAAAACTATATATTATATGT
* *
75481 TTTTAAAAATAAGTTTTCAAAA
1 TTTCAAAAATATGTTTTCAAAA
75503 CGTATACTAT
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
37 3 0.04
38 51 0.61
39 15 0.18
40 14 0.17
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (38 bp):
TTTCAAAAATATGTTTTCAAAAACTATATATTATATGT
Found at i:75516 original size:38 final size:37
Alignment explanation
Indices: 75409--75526 Score: 134
Period size: 38 Copynumber: 3.2 Consensus size: 37
75399 ATGTTTTTAA
* *
75409 AAAAATATGTTTTCAAAAACTATAATATATATGTTTTC
1 AAAAATAAGTTTTCAAAAACTAT-ATATATACGTTTTC
* * *
75447 AAAAACACGTTTTCAAAAACTATATATTATACGTTTTT
1 AAAAATAAGTTTTCAAAAACTATATA-TATACGTTTTC
75485 AAAAATAAGTTTTC-AAAACGTATACTATATAC--TTTC
1 AAAAATAAGTTTTCAAAAAC-TATA-TATATACGTTTTC
75521 AAAAAT
1 AAAAAT
75527 TACGTTTGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
36 9 0.13
37 8 0.11
38 51 0.73
39 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (37 bp):
AAAAATAAGTTTTCAAAAACTATATATATACGTTTTC
Found at i:75553 original size:2 final size:2
Alignment explanation
Indices: 75542--75588 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
75532 TTGAAATTAT
75542 TA TA -A TA TA TA TA 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 TA TA TA TA TA TA TA
75583 TA TA TA
1 TA TA TA
75589 AAAAACCCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:76021 original size:14 final size:13
Alignment explanation
Indices: 75999--76032 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
75989 GTTTATTTAT
75999 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
76012 AAAAAGAAAAAGAA
1 AAAAA-AAAAAGAA
76026 AAGAAAA
1 AA-AAAA
76033 CTATAGCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 11 0.58
15 3 0.16
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:88245 original size:21 final size:21
Alignment explanation
Indices: 88220--88267 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
88210 GGAGCGTGAG
*
88220 GGGTATCGGTACCCCTTCATA
1 GGGTATCGATACCCCTTCATA
88241 GGGTATCGATACCCCTTCATA
1 GGGTATCGATACCCCTTCATA
88262 GGGTAT
1 GGGTAT
88268 TAGTACCTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.29
Consensus pattern (21 bp):
GGGTATCGATACCCCTTCATA
Found at i:88274 original size:21 final size:20
Alignment explanation
Indices: 88228--88274 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
88218 AGGGGTATCG
*
88228 GTACCCCTTCATAGGGTATC
1 GTACCCCTTCATAGGGTATA
88248 GATACCCCTTCATAGGGTATTA
1 G-TACCCCTTCATAGGGTA-TA
88270 GTACC
1 GTACC
88275 TGCAGTGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 21 0.88
22 2 0.08
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (20 bp):
GTACCCCTTCATAGGGTATA
Found at i:91033 original size:23 final size:22
Alignment explanation
Indices: 91005--91110 Score: 101
Period size: 23 Copynumber: 4.8 Consensus size: 22
90995 GTACCATCAG
*
91005 GGGGTATCGATACCCATTCAAA
1 GGGGTATCGATACCTATTCAAA
* *
91027 GATGGTATCCATACCTATTGC--A
1 G-GGGTATCGATACCTATT-CAAA
91049 GGGGTATCGATACCTATTCAAA
1 GGGGTATCGATACCTATTCAAA
* **
91071 GGGGGTATCGATACC-AGTCTTA
1 -GGGGTATCGATACCTATTCAAA
91093 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
91111 GCACAAAAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.01
21 28 0.41
22 9 0.13
23 29 0.43
24 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (22 bp):
GGGGTATCGATACCTATTCAAA
Found at i:91096 original size:44 final size:44
Alignment explanation
Indices: 91005--91110 Score: 126
Period size: 44 Copynumber: 2.4 Consensus size: 44
90995 GTACCATCAG
* *
91005 GGGGTATCGATACCCATTCAAAGATGGTATCCATACCTATTGCA
1 GGGGTATCGATACCTATTCAAAGAGGGTATCCATACCTATTGCA
* * *
91049 GGGGTATCGATACCTATTCAAAGGGGGTATCGATACC-AGTCT-TA
1 GGGGTATCGATACCTATTCAAAGAGGGTATCCATACCTA-T-TGCA
91093 GGGGTATCGATACTCTAT
1 GGGGTATCGATAC-CTAT
91111 GCACAAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 48 0.89
45 5 0.09
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (44 bp):
GGGGTATCGATACCTATTCAAAGAGGGTATCCATACCTATTGCA
Found at i:91098 original size:21 final size:22
Alignment explanation
Indices: 91005--91105 Score: 82
Period size: 21 Copynumber: 4.6 Consensus size: 22
90995 GTACCATCAG
* *
91005 GGGGTATCGATACCCATTCAAA
1 GGGGTATCGATACCTAGTCAAA
* * *
91027 GATGGTATCCATACCTATTGC--A
1 G-GGGTATCGATACCTAGT-CAAA
*
91049 GGGGTATCGATACCTATTCAAA
1 GGGGTATCGATACCTAGTCAAA
**
91071 GGGGGTATCGATACC-AGTCTTA
1 -GGGGTATCGATACCTAGTCAAA
91093 GGGGTATCGATAC
1 GGGGTATCGATAC
91106 TCTATGCACA
Statistics
Matches: 66, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
20 1 0.02
21 28 0.42
22 8 0.12
23 28 0.42
24 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (22 bp):
GGGGTATCGATACCTAGTCAAA
Done.