Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004530.1 Hibiscus syriacus cultivar Beakdansim tig00010004_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: 110998
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:504 original size:20 final size:21
Alignment explanation
Indices: 439--509 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
429 TATTAAAATT
* *
439 GTATTGATACCATTATTTGGG
1 GTATCGATACCATTCTTTGGG
460 GTATCGATACCATTCTTTGGG
1 GTATCGATACCATTCTTTGGG
481 GTATCGATACCATTCTTT-GG
1 GTATCGATACCATTCTTTGGG
501 GTAT-GATAC
1 GTATCGATAC
510 TACCCTTACA
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.10
20 6 0.12
21 37 0.77
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (21 bp):
GTATCGATACCATTCTTTGGG
Found at i:10383 original size:21 final size:20
Alignment explanation
Indices: 10359--10398 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10349 AGATATTCAT
10359 TTATATGTAAGAAAATATATA
1 TTATAT-TAAGAAAATATATA
* *
10380 TTATATTTAGTAAATATAT
1 TTATATTAAGAAAATATAT
10399 TTTTATTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
TTATATTAAGAAAATATATA
Found at i:10762 original size:6 final size:6
Alignment explanation
Indices: 10751--10795 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
10741 TAATATACGT
*
10751 GTCGTG GTCGTG GTCGTG ATCGTG GTCGTG GTCGTG GTCGTG GTC
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTC
10796 ATACGTGTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.02, C:0.18, G:0.47, T:0.33
Consensus pattern (6 bp):
GTCGTG
Found at i:10950 original size:21 final size:21
Alignment explanation
Indices: 10880--10950 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
10870 TATTTTTTTA
* *
10880 ACTATCACAACGACACTGTAC
1 ACTATCGCAACGACACTGTAG
* * *
10901 ACTCTCGCAACG-CGAAT-TGG
1 ACTATCGCAACGAC-ACTGTAG
**
10921 AAAATCGCAACGACACTGTAG
1 ACTATCGCAACGACACTGTAG
10942 ACTATCGCA
1 ACTATCGCA
10951 TTGCGATTCT
Statistics
Matches: 35, Mismatches: 12, Indels: 6
0.66 0.23 0.11
Matches are distributed among these distances:
20 13 0.37
21 22 0.63
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGACACTGTAG
Found at i:10976 original size:22 final size:22
Alignment explanation
Indices: 10945--11002 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
10935 ACTGTAGACT
*
10945 ATCGCATTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
10967 ATCGCGTTGCGATTCTTGGAAG
1 ATCGCGTTGCGATTCTTGGAAG
10989 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
11003 TTCTTTTGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (22 bp):
ATCGCGTTGCGATTCTTGGAAG
Found at i:11056 original size:20 final size:20
Alignment explanation
Indices: 10967--11330 Score: 171
Period size: 20 Copynumber: 17.8 Consensus size: 20
10957 TTCTTGGAAG
**
10967 ATCGCGTTGCGATTCTTGGAA
1 ATCGCGTTGCGATT-TTCTAA
10988 GATCGCGTTGCGATTTTCT--
1 -ATCGCGTTGCGATTTTCTAA
* * **
11007 TTTGACCGTTGCGATTTTCTTT
1 ATCG--CGTTGCGATTTTCTAA
* **
11029 TTAACGTTGCGATTTTCTAA
1 ATCGCGTTGCGATTTTCTAA
* *
11049 ATCGCGTTGCGATTCTCTCA
1 ATCGCGTTGCGATTTTCTAA
* * *
11069 ATCGCATTGCGATTCTATAA
1 ATCGCGTTGCGATTTTCTAA
* * *
11089 ATCGCATTGCGATTCTCTCA
1 ATCGCGTTGCGATTTTCTAA
* *
11109 GTCGCATTGCGATTTTCTTCTAA
1 ATCGCGTTGCGA--TT-TTCTAA
* * *
11132 ATCGCGTTGCGACTCTCTCA
1 ATCGCGTTGCGATTTTCTAA
* * *
11152 ATCGCATTGCGATTCTATAA
1 ATCGCGTTGCGATTTTCTAA
* * * *
11172 ATCGCATTGCGATTCTATCA
1 ATCGCGTTGCGATTTTCTAA
*
11192 ATCGCATTGCGATTTTCTTCTAA
1 ATCGCGTTGCGA--TT-TTCTAA
** **
11215 ATCGCGTTGCGAACTTGGAA
1 ATCGCGTTGCGATTTTCTAA
*
11235 GCTCGCGTTGCGATTTTCT--
1 -ATCGCGTTGCGATTTTCTAA
* * * **
11254 TTTGACCATTGCGATTTTCTTT
1 ATCG--CGTTGCGATTTTCTAA
* **
11276 TTAACGTTGCGATTTTCTAA
1 ATCGCGTTGCGATTTTCTAA
* *
11296 ATCGCGTTGCGATTTT-GAT
1 ATCGCGTTGCGATTTTCTAA
11315 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
11331 ATTGGTCATT
Statistics
Matches: 270, Mismatches: 57, Indels: 33
0.75 0.16 0.09
Matches are distributed among these distances:
18 4 0.01
19 17 0.06
20 183 0.68
21 16 0.06
22 22 0.08
23 28 0.10
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.40
Consensus pattern (20 bp):
ATCGCGTTGCGATTTTCTAA
Found at i:11079 original size:40 final size:40
Alignment explanation
Indices: 11035--11226 Score: 249
Period size: 40 Copynumber: 4.7 Consensus size: 40
11025 CTTTTTAACG
11035 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
11075 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
11115 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
11158 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
11198 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
11227 ACTTGGAAGC
Statistics
Matches: 129, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
40 75 0.58
41 2 0.02
42 4 0.03
43 48 0.37
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.37
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:11154 original size:83 final size:83
Alignment explanation
Indices: 11043--11226 Score: 341
Period size: 83 Copynumber: 2.2 Consensus size: 83
11033 CGTTGCGATT
* *
11043 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
*
11108 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
11126 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
11191 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
11209 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
11227 ACTTGGAAGC
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 98 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:11320 original size:19 final size:20
Alignment explanation
Indices: 11280--11330 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
11270 TTCTTTTTAA
*
11280 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
11300 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
11319 CGTTGCGATTTT
1 CGTTGCGATTTT
11331 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:11656 original size:23 final size:24
Alignment explanation
Indices: 11630--11676 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
11620 TTTAAAATTT
*
11630 TTAAAAGTAT-TATCTATTTTTAA
1 TTAAAAATATATATCTATTTTTAA
* *
11653 TTAAAAATATATTTTTATTTTTAA
1 TTAAAAATATATATCTATTTTTAA
11677 AATTTACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (24 bp):
TTAAAAATATATATCTATTTTTAA
Found at i:11722 original size:26 final size:25
Alignment explanation
Indices: 11673--11722 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
11663 ATTTTTATTT
* *
11673 TTAAAATTTACAAATTTATTTTTTC
1 TTAAAATTTACAAATTAATGTTTTC
*
11698 TTAAAATTTTATAAATTAATGTTTT
1 TTAAAA-TTTACAAATTAATGTTTT
11723 AATAATTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (25 bp):
TTAAAATTTACAAATTAATGTTTTC
Found at i:12914 original size:20 final size:21
Alignment explanation
Indices: 12886--12925 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
12876 ATTTTTTATA
* *
12886 TAAATATAATATAAA-AAATT
1 TAAAAATAAAATAAATAAATT
12906 TAAAAATAAAATAAATAAAT
1 TAAAAATAAAATAAATAAAT
12926 ATATTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAATAAAATAAATAAATT
Found at i:12915 original size:26 final size:26
Alignment explanation
Indices: 12885--12938 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
12875 AATTTTTTAT
12885 ATAAATATAATATAAA-A-AATTTAAAA
1 ATAAA-ATAA-ATAAATATAATTTAAAA
*
12911 ATAAAATAAATAAATATATTTTAAAA
1 ATAAAATAAATAAATATAATTTAAAA
12937 AT
1 AT
12939 TGGTATCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 5 0.20
25 5 0.20
26 15 0.60
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
ATAAAATAAATAAATATAATTTAAAA
Found at i:18839 original size:37 final size:37
Alignment explanation
Indices: 18766--18840 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
18756 GTTGAAAAAT
* *
18766 ATTTATATATTTTCTTTAAAAAGTTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAGTTAAAAATCATAAA
*
18803 ATTTATATCATTTTTTTTACAAAA-TTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAAGTTAAAAATCATAAA
18840 A
1 A
18841 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 15 0.45
39 4 0.12
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAGTTAAAAATCATAAA
Found at i:24766 original size:2 final size:2
Alignment explanation
Indices: 24759--24798 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
24749 GGAAGAGACG
24759 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
24799 TGTAAACGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26684 original size:13 final size:13
Alignment explanation
Indices: 26666--26692 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26656 TAGAATATAA
26666 AATCTTAAAATTC
1 AATCTTAAAATTC
26679 AATCTTAAAATTC
1 AATCTTAAAATTC
26692 A
1 A
26693 TTAACACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AATCTTAAAATTC
Found at i:26812 original size:14 final size:13
Alignment explanation
Indices: 26791--26817 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
26781 ATTTTTGTCT
26791 TTTGAAAAATTAC
1 TTTGAAAAATTAC
26804 TTTGAAAAATTAC
1 TTTGAAAAATTAC
26817 T
1 T
26818 CCCCCTTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTGAAAAATTAC
Found at i:36551 original size:20 final size:20
Alignment explanation
Indices: 36505--36565 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
36495 TTCCCCTGTG
*
36505 GGGGGAATCGGTTCCCTTTTAAA
1 GGGGGAATCGGTTCCC---TCAA
36528 GGGGGAATCGGTTCCCTCAA
1 GGGGGAATCGGTTCCCTCAA
* *
36548 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
36566 TGTACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.54
23 16 0.46
ACGTcount: A:0.18, C:0.23, G:0.34, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:44342 original size:17 final size:18
Alignment explanation
Indices: 44322--44358 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
44312 TGATATTCGA
44322 ATAA-TTGAATCGAATAT
1 ATAATTTGAATCGAATAT
44339 ATAATTTTGAATCGAATAT
1 ATAA-TTTGAATCGAATAT
44358 A
1 A
44359 AAATCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (18 bp):
ATAATTTGAATCGAATAT
Found at i:55974 original size:3 final size:3
Alignment explanation
Indices: 55957--56055 Score: 121
Period size: 3 Copynumber: 33.0 Consensus size: 3
55947 ATGTAACAAC
* * * *
55957 ATA ACTA ATA TTA ATA ATA ATA CTG ATA ATT ATA ATA ATA ATA ATA
1 ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
56003 AT- ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATT ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
56048 AT- ATA ATA
1 ATA ATA ATA
56056 TTTATAACTC
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.05
3 72 0.88
4 6 0.07
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:56294 original size:54 final size:54
Alignment explanation
Indices: 56211--56814 Score: 698
Period size: 54 Copynumber: 11.2 Consensus size: 54
56201 TATTTTCTTT
* *
56211 GAACAATCTTC-GACCAACGGGTTCGCTCCCTCTTGT-TTCAGGAAGTAAGAACTC
1 GAACAATCTTCTG-CCTACGGGTTCGCTCCCTCTT-TCTTCAGGGAGTAAGAACTC
* ** * * * *
56265 GAACAATCTTTTGATTATGGGTTCACTCCCTCTTGCTTCAGGGAGTGA-AACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
* * * * *
56318 GAACAATCTTCTACTTACGGGTTCGCTCCCTCTTGCTTCAAGGAGT-AGAACTT
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
* * *
56371 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTGCTTCAGGGGGTAGGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
* * * *
56425 AAAACAATCTTCTGCCTACGGGTTCGCTCCTTCTTTCTTTAGGGAGTAGGAACTC
1 -GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
* * * * **
56480 GAACAGTCTTCTG-CTAACGGGTTTGCTCTCTCTTTCTTTAGGGAGTTGGAACTC
1 GAACAATCTTCTGCCT-ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
* * *
56534 GAACAATCTTCTACCTACGGGTTCACTCCCTCTTTCTTTAGGGAGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
* * * * * *
56588 GAACAATCTGCTGCCTACAGGTTCTCTCCCTCTTTCTTTATGGAGTAGGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
* * * *
56642 GAACAATCTTCTACCTACGAGTTCGCTCCCTCTTTCTTTAGGGTGTAAGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
* * *
56696 GAACAATCTTCTGCCTACGGGTTTGCTCCCTCTTTCTTCAGGGAGTATGAACTT
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
* * * * *
56750 GAACAATCTGCTGCCTACGAGTTCACTCCCTCTTGCTTCAGGAAGT-AGAACTC
1 GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
56803 GAACAATCTTCT
1 GAACAATCTTCT
56815 TTTGCTTCAC
Statistics
Matches: 473, Mismatches: 70, Indels: 15
0.85 0.13 0.03
Matches are distributed among these distances:
52 1 0.00
53 109 0.23
54 311 0.66
55 52 0.11
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (54 bp):
GAACAATCTTCTGCCTACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAAGAACTC
Found at i:57975 original size:13 final size:13
Alignment explanation
Indices: 57959--58005 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
57949 TTAGATCTGT
*
57959 TTTTTATTTTCTC
1 TTTTTCTTTTCTC
57972 TTTTTCTTTTCT-
1 TTTTTCTTTTCTC
57984 TTTTTC-TTTCTC
1 TTTTTCTTTTCTC
57996 TTTTTCTTTT
1 TTTTTCTTTT
58006 TTTCATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 5 0.16
12 12 0.39
13 14 0.45
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTCTTTTCTC
Found at i:57978 original size:8 final size:8
Alignment explanation
Indices: 57965--58052 Score: 51
Period size: 8 Copynumber: 10.8 Consensus size: 8
57955 CTGTTTTTTA
57965 TTTTCTCT
1 TTTTCTCT
57973 TTTTCT-T
1 TTTTCTCT
*
57980 TTCTT-TTT
1 TT-TTCTCT
57988 TCTTTCTCT
1 T-TTTCTCT
57997 TTTTCT-T
1 TTTTCTCT
58004 TTTT-TCAT
1 TTTTCTC-T
58012 TTTTCAT-T
1 TTTTC-TCT
*
58020 TTTTTTCAT
1 TTTTCTC-T
*
58029 TTTTTTCATT
1 TTTTCTC--T
58039 TTTTCTCT
1 TTTTCTCT
58047 TTTTCT
1 TTTTCT
58053 TCTTCAAGCA
Statistics
Matches: 65, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
6 1 0.02
7 10 0.15
8 34 0.52
9 12 0.18
10 8 0.12
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCTCT
Found at i:57981 original size:18 final size:17
Alignment explanation
Indices: 57978--58053 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 17
57968 TCTCTTTTTC
57978 TTTTCTTTTTTCTTTCTCT
1 TTTTC-TTTTT-TTTCTCT
*
57997 TTTTC-TTTTTTTC-AT
1 TTTTCTTTTTTTTCTCT
*
58012 TTTTCATTTTTTTTCATTT
1 TTTTC-TTTTTTTTC-TCT
*
58031 TTTTC-ATTTTTTCTCT
1 TTTTCTTTTTTTTCTCT
58047 TTTTCTT
1 TTTTCTT
58054 CTTCAAGCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
15 6 0.13
16 11 0.23
17 19 0.40
19 11 0.23
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTTTTTCTCT
Found at i:57987 original size:19 final size:18
Alignment explanation
Indices: 57959--58053 Score: 70
Period size: 19 Copynumber: 5.1 Consensus size: 18
57949 TTAGATCTGT
57959 TTTTTATTTTCTCTTTTTC
1 TTTTT-TTTTCTCTTTTTC
*
57978 TTTTCTTTTT-TCTTTCTC
1 TTTT-TTTTTCTCTTTTTC
*
57996 TTTTTCTTTTTTTCATTTTTC
1 -TTTT-TTTTTCTC-TTTTTC
*
58017 ATTTTTTTTCAT-TTTTT-
1 TTTTTTTTTC-TCTTTTTC
**
58034 TCATTTTTTCTCTTTTTC
1 TTTTTTTTTCTCTTTTTC
58052 TT
1 TT
58054 CTTCAAGCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 15
0.73 0.10 0.18
Matches are distributed among these distances:
16 1 0.02
17 12 0.20
18 13 0.21
19 23 0.38
20 7 0.11
21 5 0.08
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTTTTTCTCTTTTTC
Found at i:58000 original size:12 final size:12
Alignment explanation
Indices: 57966--58004 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
57956 TGTTTTTTAT
57966 TTTCTCTTTTTC
1 TTTCTCTTTTTC
57978 TTT-TCTTTTTTC
1 TTTCTC-TTTTTC
57990 TTTCTCTTTTTC
1 TTTCTCTTTTTC
58002 TTT
1 TTT
58005 TTTTCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTCTTTTTC
Found at i:58014 original size:9 final size:9
Alignment explanation
Indices: 57996--58042 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
57986 TTTCTTTCTC
57996 TTTTTC-TT
1 TTTTTCATT
58004 TTTTTCA--
1 TTTTTCATT
58011 TTTTTCATTT
1 TTTTTCA-TT
58021 TTTTTCATT
1 TTTTTCATT
58030 TTTTTCATT
1 TTTTTCATT
58039 TTTT
1 TTTT
58043 CTCTTTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.20
8 6 0.17
9 15 0.43
10 7 0.20
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCATT
Found at i:58024 original size:10 final size:10
Alignment explanation
Indices: 58011--58042 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
58001 CTTTTTTTCA
58011 TTTTTCATTT
1 TTTTTCATTT
58021 TTTTTCA-TT
1 TTTTTCATTT
58030 TTTTTCATTT
1 TTTTTCATTT
58040 TTT
1 TTT
58043 CTCTTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:58053 original size:6 final size:6
Alignment explanation
Indices: 57959--58006 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
57949 TTAGATCTGT
* *
57959 TTTTTA TTTTCTC TTTTTC -TTTTC TTTTTTC TTTCTC TTTTTC TTTTT
1 TTTTTC TTTT-TC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTT
58007 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 5 0.14
6 21 0.58
7 10 0.28
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:64733 original size:15 final size:13
Alignment explanation
Indices: 64712--64746 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
64702 ATTCAGGACT
64712 AAAATTAAAAGATC
1 AAAATTAAAAGA-C
64726 ATAAATTAAAAGAC
1 A-AAATTAAAAGAC
64740 AAAATTA
1 AAAATTA
64747 TAAACACGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 3 0.15
15 11 0.55
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (13 bp):
AAAATTAAAAGAC
Found at i:66176 original size:34 final size:34
Alignment explanation
Indices: 66106--66177 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
66096 GTGGGAGTGG
**
66106 GGCATGGGCTGTTGAGCACTGGTTTCACGTGAGA
1 GGCATGGGCTGTTGAGCACTGACTTCACGTGAGA
* *
66140 GGCATGAGG-TGTTGAGCACTGACTTCATGTGGGA
1 GGCATG-GGCTGTTGAGCACTGACTTCACGTGAGA
66174 GGCA
1 GGCA
66178 ATAACTAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 31 0.94
35 2 0.06
ACGTcount: A:0.19, C:0.17, G:0.39, T:0.25
Consensus pattern (34 bp):
GGCATGGGCTGTTGAGCACTGACTTCACGTGAGA
Found at i:66314 original size:9 final size:9
Alignment explanation
Indices: 66297--66379 Score: 76
Period size: 9 Copynumber: 8.9 Consensus size: 9
66287 TGTAATAAAC
*
66297 ATTAGTAAT
1 ATTAATAAT
66306 ATTAATAAT
1 ATTAATAAT
*
66315 AATAATAAT
1 ATTAATAAT
*
66324 ACTAATAAT
1 ATTAATAAT
66333 ATATAATAAT
1 AT-TAATAAT
*
66343 AATAATAAT
1 ATTAATAAT
*
66352 AATAATAATT
1 ATTAATAA-T
*
66362 ATAATATAAT
1 ATTA-ATAAT
*
66372 ATTTATAA
1 ATTAATAA
66380 CTCGGACAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
9 44 0.71
10 14 0.23
11 4 0.06
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (9 bp):
ATTAATAAT
Found at i:66316 original size:3 final size:3
Alignment explanation
Indices: 66302--66372 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
66292 TAAACATTAG
* *
66302 TAA TAT TAA TAA TAA TAA TAA TAC TAA TAA TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
*
66348 TAA TAA TAA TAA TTA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
66373 TTTATAACTC
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:66759 original size:17 final size:17
Alignment explanation
Indices: 66732--66776 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
66722 TAAAGCGGCA
66732 AAAAGCTTTCAAACTTCC
1 AAAA-CTTTCAAACTTCC
66750 AAAACTTTCAAACTTCC
1 AAAACTTTCAAACTTCC
66767 AAAACTTTCA
1 AAAACTTTCA
66777 CTCCCATCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAACTTTCAAACTTCC
Found at i:66798 original size:15 final size:15
Alignment explanation
Indices: 66778--66810 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
66768 AAACTTTCAC
66778 TCCCATCTCACTGTT
1 TCCCATCTCACTGTT
66793 TCCCATCTCACTGTT
1 TCCCATCTCACTGTT
66808 TCC
1 TCC
66811 TTTTCCCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.12, C:0.42, G:0.06, T:0.39
Consensus pattern (15 bp):
TCCCATCTCACTGTT
Found at i:70490 original size:73 final size:73
Alignment explanation
Indices: 70371--70518 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 73
70361 GGTGACCTGC
*
70371 ATGTCATAATGGAAGCCTACCATTGAACAAAGGATCATTCTAAGAAAATTATAGGACTTCTTTTC
1 ATGTCATAATGGAAGCCTACCATTAAACAAAGGATCATTCTAAGAAAATTATAGGACTTCTTTTC
70436 CAATTAAT
66 CAATTAAT
*
70444 ATGTCATAATGGAAGCCTACCATTAAACCAAGGATCATTCTAAGAAAATTATAGGACTTCTTTTC
1 ATGTCATAATGGAAGCCTACCATTAAACAAAGGATCATTCTAAGAAAATTATAGGACTTCTTTTC
70509 CAATTAAT
66 CAATTAAT
70517 AT
1 AT
70519 TCCTGCATAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.32
Consensus pattern (73 bp):
ATGTCATAATGGAAGCCTACCATTAAACAAAGGATCATTCTAAGAAAATTATAGGACTTCTTTTC
CAATTAAT
Found at i:73759 original size:20 final size:21
Alignment explanation
Indices: 73734--73776 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
73724 AAATTTATTT
73734 TATTTTT-ATATTTTA-AAAAA
1 TATTTTTGAT-TTTTATAAAAA
73754 TATTTTTGATTTTTATAAAAA
1 TATTTTTGATTTTTATAAAAA
73775 TA
1 TA
73777 ATATCAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTTTTGATTTTTATAAAAA
Found at i:81276 original size:23 final size:27
Alignment explanation
Indices: 81250--81364 Score: 94
Period size: 28 Copynumber: 4.2 Consensus size: 27
81240 ATTTAATAAC
81250 AATTTT-TAA-ATAAATTA-A-ATATT
1 AATTTTGTAATATAAATTATAGATATT
*
81273 AATTTTGTAATATATATTATAGATATT
1 AATTTTGTAATATAAATTATAGATATT
* * * *
81300 AATTTAATATCAATTTTAAATAATTAAATATT
1 AATTT--TGT-AA-TATAAATTA-TAGATATT
*
81332 AATTTTGTAATATTATATTATAGATATT
1 AATTTTGTAATA-TAAATTATAGATATT
81360 AATTT
1 AATTT
81365 AATATTTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
23 6 0.08
24 3 0.04
25 7 0.10
26 1 0.01
27 10 0.14
28 13 0.18
29 9 0.13
30 4 0.06
31 6 0.08
32 12 0.17
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (27 bp):
AATTTTGTAATATAAATTATAGATATT
Found at i:81309 original size:11 final size:11
Alignment explanation
Indices: 81214--81404 Score: 70
Period size: 11 Copynumber: 16.3 Consensus size: 11
81204 GGTTTTATAT
*
81214 TTAATTTTATA
1 TTAATTTAATA
* *
81225 TTATATTTGATT
1 TTA-ATTTAATA
81237 TTAATTTAATA
1 TTAATTTAATA
**
81248 ACAATTTTTAA-A
1 TTAA--TTTAATA
* *
81260 TAAATTAAATA
1 TTAATTTAATA
81271 TTAATTTTGTAATA
1 TTAA--TT-TAATA
81285 -TATATTATAGATA
1 TTA-ATT-TA-ATA
81298 TTAATTTAATA
1 TTAATTTAATA
*
81309 TCAATTTTAA-A
1 TTAA-TTTAATA
*
81320 -TAATTAAATA
1 TTAATTTAATA
81330 TTAATTTTGTAATA
1 TTAA--TT-TAATA
81344 TTATATTATAGATA
1 TTA-ATT-TA-ATA
81358 TTAATTTAATA
1 TTAATTTAATA
*
81369 TT-TTTTAATAA
1 TTAATTTAAT-A
* *
81380 TTAAATTAATT
1 TTAATTTAATA
81391 TTAATATT-ATA
1 TTAAT-TTAATA
81402 TTA
1 TTA
81405 TAGATATTTA
Statistics
Matches: 136, Mismatches: 23, Indels: 42
0.68 0.11 0.21
Matches are distributed among these distances:
9 4 0.03
10 13 0.10
11 42 0.31
12 32 0.24
13 24 0.18
14 20 0.15
15 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAATTTAATA
Found at i:81345 original size:14 final size:14
Alignment explanation
Indices: 81267--81364 Score: 51
Period size: 14 Copynumber: 6.8 Consensus size: 14
81257 AAATAAATTA
*
81267 AATATTAATTTTGT
1 AATATTAATTTTAT
*
81281 AATA-T-ATATTAT
1 AATATTAATTTTAT
81293 AGATATTAATTTAATAT
1 A-ATATTAATTT--TAT
* *
81310 CAATTTTAAATAATTA-
1 -AATATT-AAT-TTTAT
*
81326 AATATTAATTTTGT
1 AATATTAATTTTAT
*
81340 AATATT-ATATTAT
1 AATATTAATTTTAT
81353 AGATATTAATTT
1 A-ATATTAATTT
81365 AATATTTTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 21
0.66 0.12 0.22
Matches are distributed among these distances:
12 6 0.10
13 12 0.19
14 19 0.31
15 11 0.18
17 9 0.15
18 4 0.06
19 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (14 bp):
AATATTAATTTTAT
Found at i:81353 original size:60 final size:60
Alignment explanation
Indices: 81222--81425 Score: 275
Period size: 60 Copynumber: 3.5 Consensus size: 60
81212 ATTTAATTTT
* *
81222 ATATTATATT-T-GATTTTAATTTAATAACAATTTTTAAATAAATTAAATATTAATTTTGTA
1 ATATTATATTATAGATATTAATTTAATATCAA-TTTTAAAT-AATTAAATATTAATTTTGTA
81282 ATA-TATATTATAGATATTAATTTAATATCAATTTTAAATAATTAAATATTAATTTTGTA
1 ATATTATATTATAGATATTAATTTAATATCAATTTTAAATAATTAAATATTAATTTTGTA
*
81341 ATATTATATTATAGATATTAATTTAATAT---TTTTTAATAATT-AA-ATTAA-TTT-TA
1 ATATTATATTATAGATATTAATTTAATATCAATTTTAAATAATTAAATATTAATTTTGTA
*
81394 ATATTATATTATAGATATTTAATTTTATATCA
1 ATATTATATTATAGATA-TTAATTTAATATCA
81426 TATAAATTAT
Statistics
Matches: 134, Mismatches: 4, Indels: 16
0.87 0.03 0.10
Matches are distributed among these distances:
53 19 0.14
54 14 0.10
55 5 0.04
56 2 0.01
57 11 0.08
59 29 0.22
60 37 0.28
61 17 0.13
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (60 bp):
ATATTATATTATAGATATTAATTTAATATCAATTTTAAATAATTAAATATTAATTTTGTA
Found at i:81439 original size:19 final size:18
Alignment explanation
Indices: 81415--81473 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
81405 TAGATATTTA
*
81415 ATTTTATATCATATAAATT
1 ATTTTATATTAT-TAAATT
81434 ATTTTATATTATTAAA--
1 ATTTTATATTATTAAATT
*
81450 ATTTTATATTATTTTAATT
1 ATTTTATATTA-TTAAATT
81469 ATTTT
1 ATTTT
81474 GATTTAAGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 11 0.31
17 4 0.11
18 4 0.11
19 16 0.46
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTATATTATTAAATT
Found at i:81441 original size:35 final size:35
Alignment explanation
Indices: 81396--81473 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
81386 TAATTTTAAT
* *
81396 ATTATATTATAGATATT-TAATTTTATATCATATAA
1 ATTATTTTATA-ATATTAAAATTTTATATCATATAA
* * * *
81431 ATTATTTTATATTATTAAAATTTTATATTATTTTA
1 ATTATTTTATAATATTAAAATTTTATATCATATAA
81466 ATTATTTT
1 ATTATTTT
81474 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 4 0.11
35 32 0.89
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (35 bp):
ATTATTTTATAATATTAAAATTTTATATCATATAA
Found at i:81468 original size:16 final size:16
Alignment explanation
Indices: 81414--81462 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
81404 ATAGATATTT
*
81414 AATTTTATATCATATAA
1 AATTTTATATTAT-TAA
81431 ATTATTTTATATTATTAA
1 A--ATTTTATATTATTAA
81449 AATTTTATATTATT
1 AATTTTATATTATT
81463 TTAATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 13 0.45
17 1 0.03
18 4 0.14
19 11 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTTATATTATTAA
Found at i:83996 original size:17 final size:16
Alignment explanation
Indices: 83964--83997 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
83954 AAATTATACG
83964 AATATTTTTAAAATTT
1 AATATTTTTAAAATTT
*
83980 AATATTATTTAAGATTT
1 AATATT-TTTAAAATTT
83997 A
1 A
83998 TAAATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATATTTTTAAAATTT
Found at i:84834 original size:2 final size:2
Alignment explanation
Indices: 84827--84862 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
84817 AAAGAGTGAG
84827 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
84863 TGTTTGTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88174 original size:12 final size:10
Alignment explanation
Indices: 88133--88173 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
88123 TTTATCACAC
88133 CAAATTCTCT
1 CAAATTCTCT
88143 CAAATTCTCT
1 CAAATTCTCT
88153 -AAATTTCTCT
1 CAAA-TTCTCT
*
88163 CAAATACTCT
1 CAAATTCTCT
88173 C
1 C
88174 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:88426 original size:111 final size:110
Alignment explanation
Indices: 88294--88514 Score: 397
Period size: 111 Copynumber: 2.0 Consensus size: 110
88284 TAGAAATCAT
* *
88294 ATATCTCTACACTTTGCTGATACGGTGACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
88359 TATTTAGTTGATTTATTATATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTA-ATGCATGATTATTAGATTAAGAATTAA
88405 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
88470 TAATTAGTTGATTCATTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTAATGCATGATTATTAGATTAAGAATTAA
88515 TTTTTGTAAT
Statistics
Matches: 106, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
110 27 0.25
111 79 0.75
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (110 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTAATGCATGATTATTAGATTAAGAATTAA
Found at i:90013 original size:18 final size:18
Alignment explanation
Indices: 89990--90025 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
89980 CCCAGCAGCA
89990 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
90008 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
90026 TCATCGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:90653 original size:35 final size:33
Alignment explanation
Indices: 90614--90698 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
90604 ATATTTTAGT
*
90614 TAATTTTGTT-TATTACCATTTTATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
90649 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
90684 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
90699 TAAATATCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:93680 original size:23 final size:23
Alignment explanation
Indices: 93643--93720 Score: 122
Period size: 23 Copynumber: 3.4 Consensus size: 23
93633 CGTATAATTG
93643 CGAAGTG-CACGTAGAATTGCAC
1 CGAAGTGCCACGTAGAATTGCAC
93665 CGAAGTGCCACGTAGAATTGCAC
1 CGAAGTGCCACGTAGAATTGCAC
* *
93688 CGGAGTGCCGCGTAGAATTGCAC
1 CGAAGTGCCACGTAGAATTGCAC
*
93711 CGTAGTGCCA
1 CGAAGTGCCA
93721 TATAATAATG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 7 0.14
23 44 0.86
ACGTcount: A:0.27, C:0.26, G:0.29, T:0.18
Consensus pattern (23 bp):
CGAAGTGCCACGTAGAATTGCAC
Found at i:93916 original size:101 final size:103
Alignment explanation
Indices: 93736--93950 Score: 348
Period size: 101 Copynumber: 2.1 Consensus size: 103
93726 TAATGTCCAT
*
93736 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
*
93801 GACTTCACATATGTTCCAAAGAATACATATA-GTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
93838 AAGTACCACATATTATTCCTTAAGAATCATATACATAT-GT-GAAGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAG-AGATCAAGTATGTGTCTCACC
93901 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
93940 AAGGA-CACATA
1 AAGGACCACATA
93951 GACCCTCGAC
Statistics
Matches: 105, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
100 1 0.01
101 58 0.55
102 46 0.44
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:95319 original size:22 final size:21
Alignment explanation
Indices: 95294--95353 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
95284 TTCGCTTGAG
*
95294 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
95316 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
95336 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
95354 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:104743 original size:3 final size:3
Alignment explanation
Indices: 104735--104782 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
104725 CGAAACTATA
* *
104735 TAT TAT TAT TA- TAT TAC AAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
104781 TA
1 TA
104783 AAAAACTGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:104749 original size:11 final size:11
Alignment explanation
Indices: 104733--104780 Score: 69
Period size: 11 Copynumber: 4.3 Consensus size: 11
104723 TCCGAAACTA
104733 TATATTATTAT
1 TATATTATTAT
**
104744 TATATTACAAT
1 TATATTATTAT
104755 TATATTATTAT
1 TATATTATTAT
104766 TATTATTATTAT
1 TA-TATTATTAT
104778 TAT
1 TAT
104781 TAAAAAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTATTAT
Done.