Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004627.1 Hibiscus syriacus cultivar Beakdansim tig00010353_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: 85649
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:9560 original size:23 final size:23
Alignment explanation
Indices: 9510--9635 Score: 105
Period size: 23 Copynumber: 5.4 Consensus size: 23
9500 CACCGAAGTG
9510 CCGCGTAGAATATG-CACTGAAGTG-
1 CCGCGTAGAA-ATGTC-CTGAAG-GA
*
9534 CCACGTAGAAATGTCCTGAAGGA
1 CCGCGTAGAAATGTCCTGAAGGA
* * * * * *
9557 CCACATAGAATTTTCCCGAAGGG
1 CCGCGTAGAAATGTCCTGAAGGA
*
9580 CCGCGTAGAAATGT-CTCGAAGGG
1 CCGCGTAGAAATGTCCT-GAAGGA
**
9603 CCGCGTAGAAATGTCCCAAAGGA
1 CCGCGTAGAAATGTCCTGAAGGA
9626 CCGCGTAGAA
1 CCGCGTAGAA
9636 CCCTCAATTC
Statistics
Matches: 84, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.02
23 71 0.85
24 11 0.13
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (23 bp):
CCGCGTAGAAATGTCCTGAAGGA
Found at i:9589 original size:46 final size:46
Alignment explanation
Indices: 9528--9635 Score: 119
Period size: 46 Copynumber: 2.3 Consensus size: 46
9518 AATATGCACT
* * * *
9528 GAAGTGCCACGTAGAAATGTC-CTGAAGGACCACATAGAATTTTCCC
1 GAAGGGCCGCGTAGAAATGTCTC-GAAGGACCACATAGAAATGTCCC
* * *
9574 GAAGGGCCGCGTAGAAATGTCTCGAAGGGCCGCGTAGAAATGTCCC
1 GAAGGGCCGCGTAGAAATGTCTCGAAGGACCACATAGAAATGTCCC
* *
9620 AAAGGACCGCGTAGAA
1 GAAGGGCCGCGTAGAA
9636 CCCTCAATTC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 51 0.98
47 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (46 bp):
GAAGGGCCGCGTAGAAATGTCTCGAAGGACCACATAGAAATGTCCC
Found at i:10371 original size:15 final size:15
Alignment explanation
Indices: 10348--10417 Score: 122
Period size: 15 Copynumber: 4.7 Consensus size: 15
10338 TTGTCCATTA
10348 GTATCGATGCCCTTG
1 GTATCGATGCCCTTG
*
10363 GTATTGATGCCCTTG
1 GTATCGATGCCCTTG
*
10378 GTATTGATGCCCTTG
1 GTATCGATGCCCTTG
10393 GTATCGATGCCCTTG
1 GTATCGATGCCCTTG
10408 GTATCGATGC
1 GTATCGATGC
10418 TACTCCTTCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.14, C:0.23, G:0.27, T:0.36
Consensus pattern (15 bp):
GTATCGATGCCCTTG
Found at i:13782 original size:93 final size:91
Alignment explanation
Indices: 13641--13826 Score: 241
Period size: 93 Copynumber: 2.0 Consensus size: 91
13631 TATATGTGGA
* * * *
13641 TTCCTCAAATTTTGGGTCTTAAGACGTCACATACTATACTTATACATGGACGGACCTGAATATA-
1 TTCCTCAAATTTTGGATCCTAAGACGTAACATACTATACTTATACATGGACGGACCTGAA-ACAC
* *
13705 TTGTACATGAACGGGTGTGAATTGGGGT
65 TTGTACATGAACGGG-CTGAATTAGGGT
** *
13733 TTCCTC-AATTTTGGATCCTAAGACGAGTAACATGTTATACTTATACATGGACGGGCCTGAAACA
1 TTCCTCAAATTTTGGATCCTAAGAC--GTAACATACTATACTTATACATGGACGGACCTGAAACA
13797 CTTGTACATGAACGGGCTGAATTAGGGT
64 CTTGTACATGAACGGGCTGAATTAGGGT
13825 TT
1 TT
13827 GATTTGGTTG
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
91 16 0.20
92 20 0.24
93 46 0.56
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (91 bp):
TTCCTCAAATTTTGGATCCTAAGACGTAACATACTATACTTATACATGGACGGACCTGAAACACT
TGTACATGAACGGGCTGAATTAGGGT
Found at i:13799 original size:25 final size:24
Alignment explanation
Indices: 13771--13817 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
13761 AACATGTTAT
*
13771 ACTTATACATGGACGGGCCTGAAAC
1 ACTTATACATGAACGGG-CTGAAAC
*
13796 ACTTGTACATGAACGGGCTGAA
1 ACTTATACATGAACGGGCTGAA
13818 TTAGGGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (24 bp):
ACTTATACATGAACGGGCTGAAAC
Found at i:15314 original size:16 final size:16
Alignment explanation
Indices: 15295--15328 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
15285 TAAATTGCAC
*
15295 TGATATTTACTTAACT
1 TGATATTTACCTAACT
15311 TGATATTTACCTAACT
1 TGATATTTACCTAACT
15327 TG
1 TG
15329 TAAGTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (16 bp):
TGATATTTACCTAACT
Found at i:15578 original size:19 final size:19
Alignment explanation
Indices: 15554--15590 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15544 CCATCATTAT
* *
15554 ATTACTAGATTTACTTTAA
1 ATTACTAAATTAACTTTAA
15573 ATTACTAAATTAACTTTA
1 ATTACTAAATTAACTTTA
15591 TATATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTACTAAATTAACTTTAA
Found at i:16442 original size:57 final size:57
Alignment explanation
Indices: 16368--16483 Score: 187
Period size: 57 Copynumber: 2.0 Consensus size: 57
16358 ATTCATTTAT
* *
16368 ATGCTTGCTAAAATTTATGAAAATTAATCAAAAAGCATTAAATGTAAAAGCAGTAGC
1 ATGCTTACTAAAATTTATGAAAATTAATCAAAAAGCAGTAAATGTAAAAGCAGTAGC
* * *
16425 ATGCTTACTGAAATTTATGAAAATTAATGAAAAAGCAGTAAATGTAAAAGCAGTGGC
1 ATGCTTACTAAAATTTATGAAAATTAATCAAAAAGCAGTAAATGTAAAAGCAGTAGC
16482 AT
1 AT
16484 CTACAATAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (57 bp):
ATGCTTACTAAAATTTATGAAAATTAATCAAAAAGCAGTAAATGTAAAAGCAGTAGC
Found at i:18901 original size:64 final size:63
Alignment explanation
Indices: 18833--18975 Score: 166
Period size: 64 Copynumber: 2.3 Consensus size: 63
18823 TAATAGACTT
*
18833 ATAAGTGACCAAAATAT-AATCAAACAAAAACAACACATCATAATTAAAATAAAACT-AAATGTA
1 ATAAGTGACCAAAATATGAA-CAAACAAAAACAACACATCAAAATTAAAATAAAA-TAAAATGT-
18896 A
63 A
** * * *
18897 ATAAGTGACCAAGTTATGAACAAACAAAAATAGCATATCAAAATTAAAATAAAATAAAAATGTA
1 ATAAGTGACCAAAATATGAACAAACAAAAACAACACATCAAAATTAAAATAAAAT-AAAATGTA
*
18961 A-AAGTGACTAAAATA
1 ATAAGTGACCAAAATA
18976 AAATAAAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
63 12 0.18
64 47 0.70
65 8 0.12
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.21
Consensus pattern (63 bp):
ATAAGTGACCAAAATATGAACAAACAAAAACAACACATCAAAATTAAAATAAAATAAAATGTA
Found at i:19404 original size:2 final size:2
Alignment explanation
Indices: 19389--19475 Score: 99
Period size: 2 Copynumber: 44.0 Consensus size: 2
19379 TGGAGAGTTC
* * * *
19389 AT AT AT AGT TT AT AT AT A- AT AT AT AA AT AT AA ACT AT AC AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
19432 -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19472 AT AT
1 AT AT
19476 TATTATTTCA
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
1 3 0.04
2 67 0.93
3 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24935 original size:19 final size:19
Alignment explanation
Indices: 24906--24948 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
24896 GTTCTTCTTC
*
24906 TTTTGTTTTCAT-TTTTAT
1 TTTTATTTTCATGTTTTAT
24924 TATTTATTTTCATGTTTTAT
1 T-TTTATTTTCATGTTTTAT
24944 TTTTA
1 TTTTA
24949 AATATGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 14 0.64
20 7 0.32
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTATTTTCATGTTTTAT
Found at i:27544 original size:2 final size:2
Alignment explanation
Indices: 27539--27615 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
27529 ATGATACGAT
27539 TA TA TA 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
*
27581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27616 GGTTATGATC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:33096 original size:24 final size:21
Alignment explanation
Indices: 33046--33099 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 21
33036 TGATTGGACA
33046 AAAATATTATTTTTTTAATGT
1 AAAATATTATTTTTTTAATGT
*
33067 ATAATATCTATTTTTTAATAAT-T
1 AAAATAT-TATTTTTT--TAATGT
33090 CAAAATATTA
1 -AAAATATTA
33100 AATATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.22
22 8 0.30
23 3 0.11
24 10 0.37
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
AAAATATTATTTTTTTAATGT
Found at i:33110 original size:16 final size:15
Alignment explanation
Indices: 33091--33124 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
33081 TTAATAATTC
*
33091 AAAATATTAAATATTA
1 AAAATATAAAATA-TA
33107 AAAATATAAAATATA
1 AAAATATAAAATATA
33122 AAA
1 AAA
33125 TAATTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATATAAAATATA
Found at i:34558 original size:19 final size:20
Alignment explanation
Indices: 34534--34581 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
34524 GTAAAACATC
*
34534 AAATAATAAC-AAATGATGG
1 AAATAATAACAAAATGATAG
34553 AAATAATAACAAAATGATAG
1 AAATAATAACAAAATGATAG
34573 AAATAATAA
1 AAATAATAA
34582 TGTTTTCGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.21
Consensus pattern (20 bp):
AAATAATAACAAAATGATAG
Found at i:34920 original size:16 final size:16
Alignment explanation
Indices: 34896--34972 Score: 127
Period size: 16 Copynumber: 4.8 Consensus size: 16
34886 TAATAAATAA
*
34896 ACGATCATAAACGAAC
1 ACGAACATAAACGAAC
34912 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
34928 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
34944 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
34960 ATGAACATAAACG
1 ACGAACATAAACG
34973 TTGGATATCC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 57 1.00
ACGTcount: A:0.55, C:0.22, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:37983 original size:139 final size:139
Alignment explanation
Indices: 37733--38013 Score: 562
Period size: 139 Copynumber: 2.0 Consensus size: 139
37723 GGGGGGGATT
37733 TATTTAGTGTTAATCATTAAGCCATTAGCAATCAATATCTTATATGAGTCAAATTGTGATCTTAT
1 TATTTAGTGTTAATCATTAAGCCATTAGCAATCAATATCTTATATGAGTCAAATTGTGATCTTAT
37798 ATAGTTTGTTGCCTTTAAATTTAAGAATTATCTTATATTTTTTATAAGAAATAAATCAAGGCGAT
66 ATAGTTTGTTGCCTTTAAATTTAAGAATTATCTTATATTTTTTATAAGAAATAAATCAAGGCGAT
37863 TATAAGGCA
131 TATAAGGCA
37872 TATTTAGTGTTAATCATTAAGCCATTAGCAATCAATATCTTATATGAGTCAAATTGTGATCTTAT
1 TATTTAGTGTTAATCATTAAGCCATTAGCAATCAATATCTTATATGAGTCAAATTGTGATCTTAT
37937 ATAGTTTGTTGCCTTTAAATTTAAGAATTATCTTATATTTTTTATAAGAAATAAATCAAGGCGAT
66 ATAGTTTGTTGCCTTTAAATTTAAGAATTATCTTATATTTTTTATAAGAAATAAATCAAGGCGAT
38002 TATAAGGCA
131 TATAAGGCA
38011 TAT
1 TAT
38014 ATATATGCTC
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 142 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (139 bp):
TATTTAGTGTTAATCATTAAGCCATTAGCAATCAATATCTTATATGAGTCAAATTGTGATCTTAT
ATAGTTTGTTGCCTTTAAATTTAAGAATTATCTTATATTTTTTATAAGAAATAAATCAAGGCGAT
TATAAGGCA
Found at i:38581 original size:22 final size:22
Alignment explanation
Indices: 38556--38598 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
38546 TGAATTATGT
38556 ACAGAAGCAATCTAAGTGTAGG
1 ACAGAAGCAATCTAAGTGTAGG
*
38578 ACAGAAGCAATCTCAGTGTAG
1 ACAGAAGCAATCTAAGTGTAG
38599 ATTGTTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.19
Consensus pattern (22 bp):
ACAGAAGCAATCTAAGTGTAGG
Found at i:44720 original size:31 final size:31
Alignment explanation
Indices: 44677--44746 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 31
44667 TTATTAATTT
* **
44677 ATTATTTTTAAATACT-AATTATTTAATCACTA
1 ATTA-TTTTAAATA-TAAATTATATAAAAACTA
44709 ATTATTTTAAATATAAATTATATAAAAACTA
1 ATTATTTTAAATATAAATTATATAAAAACTA
44740 ATTATTT
1 ATTATTT
44747 ACATAAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 1 0.03
31 29 0.85
32 4 0.12
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTATTTTAAATATAAATTATATAAAAACTA
Found at i:45155 original size:26 final size:27
Alignment explanation
Indices: 45099--45158 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
45089 TAAGATGTTG
*
45099 TTACACAATGTTAAACTCTTTTAGTTA
1 TTACACAATGTAAAACTCTTTTAGTTA
45126 TTACACAATGTAAAACTCTTTTAGTT-
1 TTACACAATGTAAAACTCTTTTAGTTA
45152 TTACACA
1 TTACACA
45159 GGTTTAGGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 7 0.22
27 25 0.78
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.42
Consensus pattern (27 bp):
TTACACAATGTAAAACTCTTTTAGTTA
Found at i:46899 original size:36 final size:36
Alignment explanation
Indices: 46857--46926 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
46847 CTTTAATTTA
* *
46857 GGGTTTAGAATGTAATTAAAGTATTTTGGAATTTGG
1 GGGTTTAGAAGGTAATTAAAGTATTTTCGAATTTGG
* * *
46893 GGGTTTATAAGGTAATTGAAGTGTTTTCGAATTT
1 GGGTTTAGAAGGTAATTAAAGTATTTTCGAATTT
46927 TGAACATGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.29, C:0.01, G:0.27, T:0.43
Consensus pattern (36 bp):
GGGTTTAGAAGGTAATTAAAGTATTTTCGAATTTGG
Found at i:49329 original size:138 final size:138
Alignment explanation
Indices: 49078--49445 Score: 506
Period size: 138 Copynumber: 2.7 Consensus size: 138
49068 CTTTACCCTT
* * *
49078 AATTTT-ACTCAATTATGTGATTTAAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGATCAAA
1 AATTTTAAC-CAATTATTTGATTTAAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGAACAAA
* * * *
49142 TTAAAAAAT-CCTTAATTTTAAGGATTAAGTTTGAAATTAAGCCTAAAATGGAGGCTCTAATTAT
65 TTAAAAATTCCCCTAA-TTTAAGGACTAAGTTTGAAATCAAGCCTAAAATGGAGGCTCTAATTAT
49206 TAAACTAGTC
129 TAAACTAGTC
* * * * *
49216 AATTTTAACCAATTATTTGATTTGAACAATTAAAAAGGAACCTCGAGGAAAAGCGAGGACCAAAT
1 AATTTTAACCAATTATTTGATTTAAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGAACAAAT
* * * *
49281 TAAAAATTCCCCTAATTTAATGACTACGTTTGAAATCAAGCTTCAAATGGAGGCTCTAATTATTA
66 TAAAAATTCCCCTAATTTAAGGACTAAGTTTGAAATCAAGCCTAAAATGGAGGCTCTAATTATTA
*
49346 ACCTAGTC
131 AACTAGTC
* * * *
49354 AATTTTAACTATTTATTTGATTCAAATAATTAAAATGGAACCTCAAGCAAAAGCGAGGAACAAAT
1 AATTTTAACCAATTATTTGATTTAAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGAACAAAT
*
49419 TACAAATTCCCCTAATTTAAGGACTAA
66 TAAAAATTCCCCTAATTTAAGGACTAA
49446 TTTAAAAAGG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
138 193 0.96
139 7 0.04
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (138 bp):
AATTTTAACCAATTATTTGATTTAAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGAACAAAT
TAAAAATTCCCCTAATTTAAGGACTAAGTTTGAAATCAAGCCTAAAATGGAGGCTCTAATTATTA
AACTAGTC
Found at i:49759 original size:14 final size:13
Alignment explanation
Indices: 49716--49778 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
49706 TAATTCAAAA
49716 AAATTAAA-GCTAG
1 AAATTAAAGGCT-G
*
49729 AATTTAAAGGACTG
1 AAATTAAAGG-CTG
*
49743 AAATATAAATGCTG
1 AAAT-TAAAGGCTG
*
49757 AAATTTAAAGGTTG
1 AAA-TTAAAGGCTG
49771 AAATTAAA
1 AAATTAAA
49779 ATAACAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 12 0.29
14 21 0.51
15 8 0.20
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.29
Consensus pattern (13 bp):
AAATTAAAGGCTG
Found at i:52624 original size:8 final size:7
Alignment explanation
Indices: 52614--52659 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
52604 TTATTTTCTT
52614 TTTTTCA
1 TTTTTCA
52621 TTTTTCA
1 TTTTTCA
52628 TTTTTCA
1 TTTTTCA
*
52635 -TTTTCC
1 TTTTTCA
52641 TTTTTC-
1 TTTTTCA
52647 TTATTTC-
1 TT-TTTCA
52654 TTTTTC
1 TTTTTC
52660 TTCTTTTTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
6 11 0.31
7 25 0.69
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:52638 original size:13 final size:13
Alignment explanation
Indices: 52594--52659 Score: 55
Period size: 13 Copynumber: 4.9 Consensus size: 13
52584 TGAGGATTTG
52594 TTTTCATTTATT-A
1 TTTTCATTT-TTCA
*
52607 TTTTCTTTTTTTCA
1 TTTTC-ATTTTTCA
52621 TTTTTCATTTTTCA
1 -TTTTCATTTTTCA
* *
52635 TTTTCCTTTTTCT
1 TTTTCATTTTTCA
52648 TATTTC-TTTTTC
1 T-TTTCATTTTTC
52660 TTCTTTTTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
13 25 0.56
14 15 0.33
15 5 0.11
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:52651 original size:43 final size:44
Alignment explanation
Indices: 52604--52695 Score: 111
Period size: 43 Copynumber: 2.1 Consensus size: 44
52594 TTTTCATTTA
* *
52604 TTATTTTCTTTTT-TTCATTTTTCAT-TTTTCA-TTTTCCTTTTTC
1 TTATTTTCTTTTTCTTC-TTTTTCCTATTCT-ATTTTTCCTTTTTC
*
52647 TTA-TTTCTTTTTCTTCTTTTTCCTATTCTATTTTTTCTTTTTC
1 TTATTTTCTTTTTCTTCTTTTTCCTATTCTATTTTTCCTTTTTC
52690 TTATTT
1 TTATTT
52696 AAATAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
42 17 0.40
43 23 0.55
44 2 0.05
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (44 bp):
TTATTTTCTTTTTCTTCTTTTTCCTATTCTATTTTTCCTTTTTC
Found at i:52661 original size:13 final size:13
Alignment explanation
Indices: 52614--52659 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
52604 TTATTTTCTT
52614 TTTTTCATTTTTC
1 TTTTTCATTTTTC
*
52627 ATTTTTCATTTTCC
1 -TTTTTCATTTTTC
52641 TTTTTC-TTATTTC
1 TTTTTCATT-TTTC
52654 TTTTTC
1 TTTTTC
52660 TTCTTTTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 2 0.07
13 15 0.52
14 12 0.41
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTCATTTTTC
Found at i:52668 original size:15 final size:14
Alignment explanation
Indices: 52607--52691 Score: 59
Period size: 15 Copynumber: 5.9 Consensus size: 14
52597 TCATTTATTA
52607 TTTTCTTTTT-TTCAT
1 TTTTCTTTTTCTT--T
*
52622 TTTTCATTTTTC-AT
1 TTTTC-TTTTTCTTT
*
52636 TTTCCTTTTTC-TT
1 TTTTCTTTTTCTTT
*
52649 ATTTCTTTTTCTTCT
1 TTTTCTTTTTCTT-T
* *
52664 TTTTCCTATTCTATT
1 TTTTCTTTTTCT-TT
52679 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
52692 ATTTAAATAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
13 16 0.29
14 7 0.13
15 26 0.47
16 6 0.11
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:52675 original size:21 final size:21
Alignment explanation
Indices: 52609--52694 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 21
52599 ATTTATTATT
*
52609 TTCT-TTTTTTCATTTTTCATTT
1 TTCTATTTTTTC-TTTTTC-TTA
*
52631 TTC-A-TTTTCCTTTTTCTTA
1 TTCTATTTTTTCTTTTTCTTA
*
52650 TTTCT-TTTTCTTCTTTTTCCTA
1 -TTCTATTTT-TTCTTTTTCTTA
52672 TTCTATTTTTTCTTTTTCTTA
1 TTCTATTTTTTCTTTTTCTTA
52693 TT
1 TT
52695 TAAATAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
19 2 0.04
20 9 0.17
21 25 0.47
22 17 0.32
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.74
Consensus pattern (21 bp):
TTCTATTTTTTCTTTTTCTTA
Found at i:53083 original size:39 final size:39
Alignment explanation
Indices: 53040--53133 Score: 170
Period size: 39 Copynumber: 2.4 Consensus size: 39
53030 AGGTCAAACA
*
53040 AGTTCTTCTCATTATGGACTTCTTCTCCCTCTTCGGACG
1 AGTTCTTCTCATTATGGACTTATTCTCCCTCTTCGGACG
53079 AGTTCTTCTCATTATGGACTTATTCTCCCTCTTCGGACG
1 AGTTCTTCTCATTATGGACTTATTCTCCCTCTTCGGACG
*
53118 AGCTCTTCTCATTATG
1 AGTTCTTCTCATTATG
53134 AACCCTTCCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (39 bp):
AGTTCTTCTCATTATGGACTTATTCTCCCTCTTCGGACG
Found at i:53087 original size:22 final size:22
Alignment explanation
Indices: 53059--53127 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
53049 CATTATGGAC
53059 TTCTTCTCCCTCTTCGGACGAG
1 TTCTTCTCCCTCTTCGGACGAG
*
53081 TTCTTCT-CAT-TAT-GGAC---
1 TTCTTCTCCCTCT-TCGGACGAG
*
53098 TTATTCTCCCTCTTCGGACGAG
1 TTCTTCTCCCTCTTCGGACGAG
*
53120 CTCTTCTC
1 TTCTTCTC
53128 ATTATGAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
17 6 0.17
18 3 0.09
19 5 0.14
20 5 0.14
21 3 0.09
22 13 0.37
ACGTcount: A:0.12, C:0.33, G:0.14, T:0.41
Consensus pattern (22 bp):
TTCTTCTCCCTCTTCGGACGAG
Found at i:53237 original size:158 final size:159
Alignment explanation
Indices: 52920--53255 Score: 530
Period size: 158 Copynumber: 2.1 Consensus size: 159
52910 AGGTTGAACA
* * *
52920 AGTTCTTCTCATTATGAACTTATCTCCCCCTCTTCGGAAGAGTTCTTCTCATTATGAACTCTTTC
1 AGTTCTTCTCATTATGAACTTATCTCCCCCTCTTCGGAAGAGCTCTTCTCATTATGAACCCTTCC
* * * *
52985 ATTGGAAATGATTACCCACCTCCTTCTGTGTTGGATTTGAGTAAAAGGTCAAACAAGTTCTTCTC
66 ATTGGAAATGATGACCCACATCCTTCTGTGATGGATTTGAGCAAAAGGTCAAACAAGTTCTTCTC
* *
53050 ATTATGGACTTCTTCTCCCTCTTCGGACG
131 ATTATGAACTTCTTCTCCCTCTTCAGACG
* * *
53079 AGTTCTTCTCATTATGGACTTAT-TCTCCCTCTTCGGACGAGCTCTTCTCATTATGAACCCTTCC
1 AGTTCTTCTCATTATGAACTTATCTCCCCCTCTTCGGAAGAGCTCTTCTCATTATGAACCCTTCC
* * *
53143 ATTGGAAATGATGATCCACATCCTTCTGTGATGGATTTGAGCAAAAGGTCGAACAAGTTCTTCTT
66 ATTGGAAATGATGACCCACATCCTTCTGTGATGGATTTGAGCAAAAGGTCAAACAAGTTCTTCTC
53208 ATTATGAACTTCTTCTCCCTCTTCAGACG
131 ATTATGAACTTCTTCTCCCTCTTCAGACG
53237 AGTTCTTCTCATTATGAAC
1 AGTTCTTCTCATTATGAAC
53256 CATTCTTCTC
Statistics
Matches: 161, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
158 139 0.86
159 22 0.14
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (159 bp):
AGTTCTTCTCATTATGAACTTATCTCCCCCTCTTCGGAAGAGCTCTTCTCATTATGAACCCTTCC
ATTGGAAATGATGACCCACATCCTTCTGTGATGGATTTGAGCAAAAGGTCAAACAAGTTCTTCTC
ATTATGAACTTCTTCTCCCTCTTCAGACG
Found at i:53261 original size:19 final size:19
Alignment explanation
Indices: 53239--53279 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
53229 TTCAGACGAG
53239 TTCTTCTCATTATGAACCA
1 TTCTTCTCATTATGAACCA
53258 TTCTTCTCATTATGAACCA
1 TTCTTCTCATTATGAACCA
53277 TTC
1 TTC
53280 CATTGGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.44
Consensus pattern (19 bp):
TTCTTCTCATTATGAACCA
Found at i:53310 original size:138 final size:138
Alignment explanation
Indices: 53121--53394 Score: 440
Period size: 138 Copynumber: 2.0 Consensus size: 138
53111 TCGGACGAGC
* *
53121 TCTTCTCATTATGAACCCTTCCATTGGAAATGATGATCCACATCCTTCTGTGATGGATTTGAGCA
1 TCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACATCATTCTGTGATGGATTTGAGCA
* * *
53186 AAAGGTCGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCTTCAGACGAGTTCTTCTCATTA
66 AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATTCAGACGAGTTCTTCTCATTA
53251 TGAACCAT
131 TGAACCAT
* *
53259 TCTTCTCATTATGAACCATTCCATTGGGAATGATGATCCACCTCATTCTGTGATGGATTTGAGCA
1 TCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACATCATTCTGTGATGGATTTGAGCA
* * * * *
53324 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTCCTTATTCGGACGAGTTCTTCTCATTA
66 AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATTCAGACGAGTTCTTCTCATTA
53389 TGAACC
131 TGAACC
53395 CTTTCATTAG
Statistics
Matches: 124, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 124 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (138 bp):
TCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACATCATTCTGTGATGGATTTGAGCA
AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATTCAGACGAGTTCTTCTCATTA
TGAACCAT
Found at i:53982 original size:36 final size:35
Alignment explanation
Indices: 53912--54003 Score: 87
Period size: 36 Copynumber: 2.6 Consensus size: 35
53902 AAATGATTTC
* * * * *
53912 GTTTTAAGAGAGACTATCTCAAGCGAGATGAAATT
1 GTTTTAAGAAAAACAATCTCAAGCAAGATAAAATT
*
53947 GGTTTTAAGAAAAACAATCTCAAGTAAGATAAAATT
1 -GTTTTAAGAAAAACAATCTCAAGCAAGATAAAATT
* * *
53983 -TTTCAAGTAAAACAATTTCAA
1 GTTTTAAGAAAAACAATCTCAA
54004 AATTTGTGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 18 0.38
36 29 0.62
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (35 bp):
GTTTTAAGAAAAACAATCTCAAGCAAGATAAAATT
Found at i:54124 original size:21 final size:22
Alignment explanation
Indices: 54065--54113 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
54055 AAAAACAATC
*
54065 TCAAGTGAGATAAATTTTTGTT
1 TCAAGGGAGATAAATTTTTGTT
54087 TCAAGGGAGATAAATTTTTGTT
1 TCAAGGGAGATAAATTTTTGTT
54109 TCAAG
1 TCAAG
54114 TGAAACAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (22 bp):
TCAAGGGAGATAAATTTTTGTT
Found at i:57124 original size:14 final size:14
Alignment explanation
Indices: 57107--57141 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
57097 ATACAAGTGC
57107 ACAAATACAAAGAT
1 ACAAATACAAAGAT
*
57121 ACAAATGCAAAGAT
1 ACAAATACAAAGAT
*
57135 GCAAATA
1 ACAAATA
57142 TTTGAATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.60, C:0.14, G:0.11, T:0.14
Consensus pattern (14 bp):
ACAAATACAAAGAT
Found at i:57154 original size:28 final size:28
Alignment explanation
Indices: 57123--57215 Score: 132
Period size: 28 Copynumber: 3.3 Consensus size: 28
57113 ACAAAGATAC
* *
57123 AAATGCAAAGATGCAAATATTTGAATGT
1 AAATGCAAAGATGCAAAGATATGAATGT
57151 AAATGCAAAGATGCAAAGATATGAATGT
1 AAATGCAAAGATGCAAAGATATGAATGT
* * * *
57179 AAATACAAAGATGCAAAGATGTAAATAT
1 AAATGCAAAGATGCAAAGATATGAATGT
57207 AAATGCAAA
1 AAATGCAAA
57216 CTGTAAAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.23
Consensus pattern (28 bp):
AAATGCAAAGATGCAAAGATATGAATGT
Found at i:59942 original size:139 final size:138
Alignment explanation
Indices: 59398--60047 Score: 670
Period size: 139 Copynumber: 4.7 Consensus size: 138
59388 AAGAATTTGA
* * * * * * *
59398 TATTAATCCAAATCATTTTTAATAAATTA-TTGAGTCGAATAATCAAAATGGAACCTCGAGCATA
1 TATTAA-CCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
* * * * * * * * * * * * * * *
59462 GGCGATGACCAAATTAAGATTTCTCTTAAATTAAAGGACTAAATATCACATTAAACTTAAGATAG
65 AGCGATGACCAAATTAAAAATTCCCCT-AATTTAATGACTAAGTTTGAAATTAAGCCTAAAATGG
* *
59527 AAGCTCT-AT
129 AGGCTATAAT
*
59536 TAATTAACCTAATTAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
1 T-ATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
* ** *
59601 AGCGAGGACCAAATTAAAAATTTGCCTAAATTTAAAT-ACCAAG--TGAAATTAAGCCTAAAATG
65 AGCGATGACCAAATTAAAAATTCCCCT-AATTT-AATGACTAAGTTTGAAATTAAGCCTAAAATG
*
59663 GAGGATATAA-
128 GAGGCTATAAT
* * * *
59673 TATTAATCCTAATTAATTTTAGTCAATTATGTGATTTGAATAATTAACATGGAACCTCGAGCAAA
1 TATTAA-CCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
* * *
59738 AGAGA-GAACCAAATTAAAAATT-CCCTAATTTTAAGGACTAAGTTTAAAATTAAGCCTAAAATG
65 AGCGATG-ACCAAATTAAAAATTCCCCTAA-TTTAATGACTAAGTTTGAAATTAAGCCTAAAATG
*
59801 GAGGCTGTAAT
128 GAGGCTATAAT
* * * * * *
59812 TATTAACCCAATCAATTTTAATCAATTATTTGATTGGAACAATTAAAAGGGGACATCGAGCAAAA
1 TATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAA
59877 GCGATGACCAAATTAAAAAATTCCCCTAATTTAATGACTAAGTTTGAAATTAAGCCTAAAATGGA
66 GCGATGACCAAATT-AAAAATTCCCCTAATTTAATGACTAAGTTTGAAATTAAGCCTAAAATGGA
* *
59942 GACTCTAAT
130 GGCTATAAT
* * * * * * *
59951 TATTAACCTAGTCAATTCTAATTAATTCTTTGATTCGAATAATTAAAATGTAACCTCAAGC-AAA
1 TATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAA
60015 GACGATGACCAAATTAAAAATTCCCCTAATTTA
66 G-CGATGACCAAATTAAAAATTCCCCTAATTTA
60048 TGGTCTAATT
Statistics
Matches: 432, Mismatches: 65, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
135 4 0.01
136 17 0.04
137 93 0.22
138 128 0.30
139 182 0.42
140 8 0.02
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (138 bp):
TATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAA
GCGATGACCAAATTAAAAATTCCCCTAATTTAATGACTAAGTTTGAAATTAAGCCTAAAATGGAG
GCTATAAT
Found at i:60368 original size:14 final size:13
Alignment explanation
Indices: 60325--60387 Score: 56
Period size: 14 Copynumber: 4.6 Consensus size: 13
60315 TAATTCAAAA
60325 AAATTAAA-GCTAG
1 AAATTAAAGGCT-G
*
60338 AATTTAAAGGACTG
1 AAATTAAAGG-CTG
*
60352 AAATATAAATGCTG
1 AAAT-TAAAGGCTG
*
60366 AAATTTAAAGGTTG
1 AAA-TTAAAGGCTG
60380 AAATTAAA
1 AAATTAAA
60388 ATAACAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
13 12 0.29
14 21 0.51
15 8 0.20
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.29
Consensus pattern (13 bp):
AAATTAAAGGCTG
Found at i:63252 original size:8 final size:7
Alignment explanation
Indices: 63242--63293 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
63232 TTATTTTCTT
63242 TTTTTCA
1 TTTTTCA
63249 TTTTTCA
1 TTTTTCA
63256 TTTTTCA
1 TTTTTCA
63263 -TTTTCA
1 TTTTTCA
*
63269 -TTTTCC
1 TTTTTCA
63275 TTTTTC-
1 TTTTTCA
63281 TTATTTC-
1 TT-TTTCA
63288 TTTTTC
1 TTTTTC
63294 TTCTTTTTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
6 17 0.40
7 25 0.60
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:63266 original size:13 final size:13
Alignment explanation
Indices: 63222--63272 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
63212 TGAGGATTTG
63222 TTTTCATTTATT-A
1 TTTTCATTT-TTCA
*
63235 TTTTCTTTTTTTCA
1 TTTTC-ATTTTTCA
63249 TTTTTCATTTTTCA
1 -TTTTCATTTTTCA
63263 TTTTCATTTT
1 TTTTCATTTT
63273 CCTTTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 17 0.52
14 11 0.33
15 5 0.15
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:63293 original size:6 final size:6
Alignment explanation
Indices: 63242--63326 Score: 57
Period size: 6 Copynumber: 13.3 Consensus size: 6
63232 TTATTTTCTT
* *
63242 TTTTTC ATTTTTC ATTTTTC ATTTTC ATTTTCC TTTTTC TTATTTC TTTTTC
1 TTTTTC -TTTTTC -TTTTTC TTTTTC -TTTTTC TTTTTC TT-TTTC TTTTTC
* *
63294 TTCTT- TTTTCC TATTCTAT- TTTTTC TTTTTC TT
1 TTTTTC TTTTTC T-TT-T-TC TTTTTC TTTTTC TT
63327 ATTTAAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
5 4 0.06
6 30 0.48
7 27 0.43
8 2 0.03
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTTC
Found at i:63295 original size:13 final size:13
Alignment explanation
Indices: 63242--63293 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
63232 TTATTTTCTT
63242 TTTTTCATTTTTCA
1 TTTTTC-TTTTTCA
*
63256 TTTTTCATTTTCA
1 TTTTTCTTTTTCA
*
63269 TTTTCCTTTTTC-
1 TTTTTCTTTTTCA
63281 TTATTTCTTTTTC
1 TT-TTTCTTTTTC
63294 TTCTTTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 2 0.06
13 25 0.76
14 6 0.18
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTTCTTTTTCA
Found at i:63310 original size:22 final size:23
Alignment explanation
Indices: 63269--63323 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
63259 TTCATTTTCA
* *
63269 TTTTCCTTTTTCTTATTTCT-TT
1 TTTTCTTTTTTCCTATTTCTATT
63291 TTCTTCTTTTTTCCTA-TTCTATT
1 TT-TTCTTTTTTCCTATTTCTATT
63314 TTTTCTTTTT
1 TTTTCTTTTT
63324 CTTATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTCTTTTTTCCTATTTCTATT
Found at i:63717 original size:39 final size:39
Alignment explanation
Indices: 63674--63767 Score: 170
Period size: 39 Copynumber: 2.4 Consensus size: 39
63664 AGGTCAAACA
*
63674 AGTTCTTCTCATTATGGACTTCTTCTCCCTCTTCGGACG
1 AGTTCTTCTCATTATGGACTTATTCTCCCTCTTCGGACG
63713 AGTTCTTCTCATTATGGACTTATTCTCCCTCTTCGGACG
1 AGTTCTTCTCATTATGGACTTATTCTCCCTCTTCGGACG
*
63752 AGCTCTTCTCATTATG
1 AGTTCTTCTCATTATG
63768 AACCCTTCCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (39 bp):
AGTTCTTCTCATTATGGACTTATTCTCCCTCTTCGGACG
Found at i:63721 original size:22 final size:22
Alignment explanation
Indices: 63693--63761 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
63683 CATTATGGAC
63693 TTCTTCTCCCTCTTCGGACGAG
1 TTCTTCTCCCTCTTCGGACGAG
*
63715 TTCTTCT-CAT-TAT-GGAC---
1 TTCTTCTCCCTCT-TCGGACGAG
*
63732 TTATTCTCCCTCTTCGGACGAG
1 TTCTTCTCCCTCTTCGGACGAG
*
63754 CTCTTCTC
1 TTCTTCTC
63762 ATTATGAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
17 6 0.17
18 3 0.09
19 5 0.14
20 5 0.14
21 3 0.09
22 13 0.37
ACGTcount: A:0.12, C:0.33, G:0.14, T:0.41
Consensus pattern (22 bp):
TTCTTCTCCCTCTTCGGACGAG
Found at i:63871 original size:158 final size:159
Alignment explanation
Indices: 63554--63889 Score: 530
Period size: 158 Copynumber: 2.1 Consensus size: 159
63544 AGGTTGAACA
* * *
63554 AGTTCTTCTCATTATGAACTTATCTCCCCCTCTTCGGAAGAGTTCTTCTCATTATGAACTCTTTC
1 AGTTCTTCTCATTATGAACTTATCTCCCCCTCTTCGGAAGAGCTCTTCTCATTATGAACCCTTCC
* * * *
63619 ATTGGAAATGATTACCCACCTCCTTCTGTGTTGGATTTGAGTAAAAGGTCAAACAAGTTCTTCTC
66 ATTGGAAATGATGACCCACATCCTTCTGTGATGGATTTGAGCAAAAGGTCAAACAAGTTCTTCTC
* *
63684 ATTATGGACTTCTTCTCCCTCTTCGGACG
131 ATTATGAACTTCTTCTCCCTCTTCAGACG
* * *
63713 AGTTCTTCTCATTATGGACTTAT-TCTCCCTCTTCGGACGAGCTCTTCTCATTATGAACCCTTCC
1 AGTTCTTCTCATTATGAACTTATCTCCCCCTCTTCGGAAGAGCTCTTCTCATTATGAACCCTTCC
* * *
63777 ATTGGAAATGATGATCCACATCCTTCTGTGATGGATTTGAGCAAAAGGTCGAACAAGTTCTTCTT
66 ATTGGAAATGATGACCCACATCCTTCTGTGATGGATTTGAGCAAAAGGTCAAACAAGTTCTTCTC
63842 ATTATGAACTTCTTCTCCCTCTTCAGACG
131 ATTATGAACTTCTTCTCCCTCTTCAGACG
63871 AGTTCTTCTCATTATGAAC
1 AGTTCTTCTCATTATGAAC
63890 CATTCTTCTC
Statistics
Matches: 161, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
158 139 0.86
159 22 0.14
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (159 bp):
AGTTCTTCTCATTATGAACTTATCTCCCCCTCTTCGGAAGAGCTCTTCTCATTATGAACCCTTCC
ATTGGAAATGATGACCCACATCCTTCTGTGATGGATTTGAGCAAAAGGTCAAACAAGTTCTTCTC
ATTATGAACTTCTTCTCCCTCTTCAGACG
Found at i:63895 original size:19 final size:19
Alignment explanation
Indices: 63873--63913 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
63863 TTCAGACGAG
63873 TTCTTCTCATTATGAACCA
1 TTCTTCTCATTATGAACCA
63892 TTCTTCTCATTATGAACCA
1 TTCTTCTCATTATGAACCA
63911 TTC
1 TTC
63914 CATTGGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.44
Consensus pattern (19 bp):
TTCTTCTCATTATGAACCA
Found at i:63944 original size:138 final size:138
Alignment explanation
Indices: 63755--64028 Score: 440
Period size: 138 Copynumber: 2.0 Consensus size: 138
63745 TCGGACGAGC
* *
63755 TCTTCTCATTATGAACCCTTCCATTGGAAATGATGATCCACATCCTTCTGTGATGGATTTGAGCA
1 TCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACATCATTCTGTGATGGATTTGAGCA
* * *
63820 AAAGGTCGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCTTCAGACGAGTTCTTCTCATTA
66 AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATTCAGACGAGTTCTTCTCATTA
63885 TGAACCAT
131 TGAACCAT
* *
63893 TCTTCTCATTATGAACCATTCCATTGGGAATGATGATCCACCTCATTCTGTGATGGATTTGAGCA
1 TCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACATCATTCTGTGATGGATTTGAGCA
* * * * *
63958 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTCCTTATTCGGACGAGTTCTTCTCATTA
66 AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATTCAGACGAGTTCTTCTCATTA
64023 TGAACC
131 TGAACC
64029 CTTTCATTAG
Statistics
Matches: 124, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 124 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (138 bp):
TCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACATCATTCTGTGATGGATTTGAGCA
AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATTCAGACGAGTTCTTCTCATTA
TGAACCAT
Found at i:64604 original size:36 final size:35
Alignment explanation
Indices: 64546--64637 Score: 87
Period size: 36 Copynumber: 2.6 Consensus size: 35
64536 AAATGATTTC
* * * * *
64546 GTTTTAAGAGAGACTATCTCAAGCGAGATGAAATT
1 GTTTTAAGAAAAACAATATCAAGCGAGATAAAATT
*
64581 GGTTTTAAGAAAAACAATATCAAGTGAGATAAAATT
1 -GTTTTAAGAAAAACAATATCAAGCGAGATAAAATT
* * *
64617 -TTTCAAGTAAAACAATTTCAA
1 GTTTTAAGAAAAACAATATCAA
64638 AATTTGTGTT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 18 0.38
36 29 0.62
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (35 bp):
GTTTTAAGAAAAACAATATCAAGCGAGATAAAATT
Found at i:64733 original size:22 final size:22
Alignment explanation
Indices: 64699--64752 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
64689 AAAAACAATC
*
64699 TCAAGTGAAATAAATTTTTGTT
1 TCAAGGGAAATAAATTTTTGTT
*
64721 TCAAGGGAGATAAATTTTTGTT
1 TCAAGGGAAATAAATTTTTGTT
*
64743 TCAAGTGAAA
1 TCAAGGGAAA
64753 CAATTTCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.39
Consensus pattern (22 bp):
TCAAGGGAAATAAATTTTTGTT
Found at i:67786 original size:28 final size:28
Alignment explanation
Indices: 67755--67830 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
67745 CAAAGATACG
*
67755 AATGCAAAGATGCAAATATTTGAATGTA
1 AATGCAAAGATGCAAATATATGAATGTA
* *
67783 AATGCAAAGTTGCAAAGATATGAATGTA
1 AATGCAAAGATGCAAATATATGAATGTA
* *
67811 AATACAAAGATGTAAATATA
1 AATGCAAAGATGCAAATATA
67831 AATGCAAACT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (28 bp):
AATGCAAAGATGCAAATATATGAATGTA
Found at i:67832 original size:20 final size:20
Alignment explanation
Indices: 67795--67838 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
67785 TGCAAAGTTG
* *
67795 CAAAGATATGAATGTAAATA
1 CAAAGATATAAATATAAATA
* *
67815 CAAAGATGTAAATATAAATG
1 CAAAGATATAAATATAAATA
67835 CAAA
1 CAAA
67839 CTGTAAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.23
Consensus pattern (20 bp):
CAAAGATATAAATATAAATA
Found at i:70510 original size:139 final size:138
Alignment explanation
Indices: 69957--70606 Score: 674
Period size: 139 Copynumber: 4.7 Consensus size: 138
69947 AAGAATCTGA
* * * * * *
69957 TATTAATCCAAATCATTTTTAAT-AACTTA-TTGAGTCGAATAATCAAAATGGAACCTCGAGCAT
1 TATTAA-CCTAATCAATTTTAATCAA-TTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAA
* * * * * * * * * * * * * * *
70020 AGGCGAGGACCAAATTAAGATTTCTCTTAAATTAAAGGACTAAATATCACATTAAACCTAAGATA
64 AAGCGATGACCAAATTAAAAATTCCCCT-AATTTAATGACTAAGTTTGAAATTAAGCCTAAAATG
* *
70085 GAAGCTCT-AT
128 GAGGATCTAAT
*
70095 TAATTAACCTAATTAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
1 T-ATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
* ** *
70160 AGCGAGGACCAAATTAAAAATTTGCCTAAATTTAAAT-ACCAAG--TGAAATTAAGCCTAAAATG
65 AGCGATGACCAAATTAAAAATTCCCCT-AATTT-AATGACTAAGTTTGAAATTAAGCCTAAAATG
*
70222 GAGGATATAA-
128 GAGGATCTAAT
* * *
70232 TATTAATCCTAATTAATTTTAGTCAATTATGTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
1 TATTAA-CCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
* * *
70297 AGAGA-GAACCAAATTAAAAATT-CCCTAATTTTAAGGACTAAGTTTAAAATTAAGCCTAAAATG
65 AGCGATG-ACCAAATTAAAAATTCCCCTAA-TTTAATGACTAAGTTTGAAATTAAGCCTAAAATG
*
70360 GAGGATGTAAT
128 GAGGATCTAAT
* * * * * *
70371 TATTAACCTAGTCAATTTTAATCAATTATTTGATTGGAACAATTAAAAGGGGACATCGAGCAAAA
1 TATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAA
70436 GCGATGACCAAATTAAAAAATTCCCCTAATTTAATGACTAAGTTTGAAATTAAGCCTAAAATGGA
66 GCGATGACCAAATT-AAAAATTCCCCTAATTTAATGACTAAGTTTGAAATTAAGCCTAAAATGGA
70501 -GACTCTAAT
130 GGA-TCTAAT
* * * * * * *
70510 TATTAACCTAGTCAATTCTAATTAATTCTTTGATTCGAATAATTAAAATGTAACCTCAAGC-AAA
1 TATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAA
70574 GACGATGACCAAATTAAAAATTCCCCTAATTTA
66 G-CGATGACCAAATTAAAAATTCCCCTAATTTA
70607 TGGTCTAATT
Statistics
Matches: 439, Mismatches: 56, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
135 4 0.01
136 17 0.04
137 95 0.22
138 130 0.30
139 185 0.42
140 8 0.02
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (138 bp):
TATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAA
GCGATGACCAAATTAAAAATTCCCCTAATTTAATGACTAAGTTTGAAATTAAGCCTAAAATGGAG
GATCTAAT
Found at i:70927 original size:13 final size:13
Alignment explanation
Indices: 70909--70945 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
70899 TTTAAAGTAC
*
70909 TGAAATTAAATGT
1 TGAAATTAAAGGT
70922 TGAAATTTAAAGGT
1 TGAAA-TTAAAGGT
70936 TGAAATTAAA
1 TGAAATTAAA
70946 ATAACAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (13 bp):
TGAAATTAAAGGT
Found at i:72687 original size:18 final size:20
Alignment explanation
Indices: 72658--72694 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
72648 TAAAACTATT
72658 TTTTATTATATTA-TATTTA
1 TTTTATTATATTATTATTTA
72677 TTTTA-TATATTATTATTT
1 TTTTATTATATTATTATTT
72695 GAATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATTATATTATTATTTA
Found at i:73689 original size:60 final size:60
Alignment explanation
Indices: 73592--73704 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
73582 TGACACGATA
* * *** *
73592 CCTTCAAGTTCCAGGGAGAGGCATTCAACTGTGAGCTTCTTCGACCTCAATGTCGAGATG
1 CCTTCAAGTTCAAGGGAGAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGAGATG
*
73652 CCTTCAAGTTCAAGGG-GAAGGCATGCAACTACCAGCTTGTTCGACCTAAATGT
1 CCTTCAAGTTCAAGGGAG-AGGCATGCAACTACCAGCTTCTTCGACCTAAATGT
73705 TGATATCATG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.02
60 44 0.98
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (60 bp):
CCTTCAAGTTCAAGGGAGAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGAGATG
Found at i:81474 original size:7 final size:7
Alignment explanation
Indices: 81462--81486 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
81452 GTCATGCATT
81462 TAAATAA
1 TAAATAA
81469 TAAATAA
1 TAAATAA
81476 TAAATAA
1 TAAATAA
81483 TAAA
1 TAAA
81487 ATGTATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAATAA
Found at i:82466 original size:24 final size:24
Alignment explanation
Indices: 82439--82484 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
82429 ATTTAATAAA
*
82439 ATTA-TGCTAATATTATTATAAAAT
1 ATTATTGCTAAAATT-TTATAAAAT
*
82463 ATTATTTCTAAAATTTTATAAA
1 ATTATTGCTAAAATTTTATAAA
82485 TAAAAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTATTGCTAAAATTTTATAAAAT
Found at i:82601 original size:23 final size:23
Alignment explanation
Indices: 82573--82620 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
82563 TATATTGTAT
82573 TTTTAAA-ATTATTAATAAATATA
1 TTTTAAATATTATTAATAAA-ATA
* *
82596 TTTTAAATATTTTTATTAAAATA
1 TTTTAAATATTATTAATAAAATA
82619 TT
1 TT
82621 ATTAGACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTAAATATTATTAATAAAATA
Found at i:82622 original size:11 final size:13
Alignment explanation
Indices: 82570--82624 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 13
82560 GAGTATATTG
*
82570 TATTTTTAAA-AT
1 TATTATTAAATAT
*
82582 TATTAATAAATA-
1 TATTATTAAATAT
82594 TATT-TTAAATAT
1 TATTATTAAATAT
*
82606 TTTTATTAAAATAT
1 TATTATT-AAATAT
82620 TATTA
1 TATTA
82625 GACTATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 6 0.18
12 15 0.44
13 3 0.09
14 10 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTATTAAATAT
Done.