Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002897.1 Hibiscus syriacus cultivar Beakdansim tig00005986_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: 131174
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:4358 original size:17 final size:17
Alignment explanation
Indices: 4336--4372 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4326 AATTTCAGTA
*
4336 TATGAAACTGAGTTTTG
1 TATGAAACTGAATTTTG
*
4353 TATGAAACTTAATTTTG
1 TATGAAACTGAATTTTG
4370 TAT
1 TAT
4373 ACTTGATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (17 bp):
TATGAAACTGAATTTTG
Found at i:7628 original size:16 final size:17
Alignment explanation
Indices: 7607--7638 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
7597 CCCAATATAA
7607 TAAATTAAT-AATTTAT
1 TAAATTAATAAATTTAT
7623 TAAATTAATAAATTTA
1 TAAATTAATAAATTTA
7639 ATGTGTGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAATTAATAAATTTAT
Found at i:7929 original size:16 final size:17
Alignment explanation
Indices: 7892--7936 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
7882 GTTTATGAGA
7892 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGT-AAG
*
7910 GAATTGAAATCTGT-AG
1 GAATTGGAATCTGTAAG
7926 GAATTGGAATC
1 GAATTGGAATC
7937 CAATTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 12 0.48
18 13 0.52
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (17 bp):
GAATTGGAATCTGTAAG
Found at i:8805 original size:268 final size:255
Alignment explanation
Indices: 8512--9058 Score: 810
Period size: 268 Copynumber: 2.1 Consensus size: 255
8502 TTCACCCTAA
* *
8512 ACCCGAACCCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCA
1 ACCCG-ACCCGACCCAAATATCACACTTAAAAAACCCGACCCGAACCGAACAAAATAAAGTTTCA
*
8577 TCCGACCTGACCCGACCCGAATATATGAATTAGAAAT-TCGACCCGACCCGACCCGAAATAATAA
65 T----CC-GACCCGACCCGAATATATAAATTAGAAATCTCGACCCGACCCGACCCGAAATAATAA
* *
8641 AAAAATATTTTTATTTAATAAAAATAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTT
125 AAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTC
8706 GGGTCGGTCCGG-TTTTTTCACCCTAAACCCAAACCCGACCCGATCCGACCCGAATATCACACTT
190 GGGTCGGTCCGGTTTTTTTCACCCTAAACCCAAACCCGA-CC--T-------GAATATCACACTT
8770 AAAAAAACCCG
245 AAAAAAACCCG
8781 ACCCGACCCGACCCAAATATCACACTTAAAAAACCCGACCCGAACCGAACAAAATAAAGTTTCAT
1 ACCCGACCCGACCCAAATATCACACTTAAAAAACCCGACCCGAACCGAACAAAATAAAGTTTCAT
8846 CCGACCCGACCCGAATATATAAATTAGAAATCCAACTCGACCCGACCCGACCCGAAATAATAAAA
66 CCGACCCGACCCGAATATATAAATTAGAAAT----CTCGACCCGACCCGACCCGAAATAATAAAA
* *
8911 AATTATTTTTATTTAATAAAAACAGTGACTTAATCCGACCTGACCCGAATTATATATATTTTCGG
127 AAATATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGG
*
8976 GTCGGTTCGGTTTTTTTCACCCTAAACCCAAACCCGACCTGAATATCACACTTAAAAAAACCCG
192 GTCGGTCCGGTTTTTTTCACCCTAAACCCAAACCCGACCTGAATATCACACTTAAAAAAACCCG
* *
9040 ATCCGACCCGACCAAAATA
1 ACCCGACCCGACCCAAATA
9059 AAGTTTCACC
Statistics
Matches: 262, Mismatches: 10, Indels: 22
0.89 0.03 0.07
Matches are distributed among these distances:
259 41 0.16
263 28 0.11
264 2 0.01
266 1 0.00
268 159 0.61
269 31 0.12
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (255 bp):
ACCCGACCCGACCCAAATATCACACTTAAAAAACCCGACCCGAACCGAACAAAATAAAGTTTCAT
CCGACCCGACCCGAATATATAAATTAGAAATCTCGACCCGACCCGACCCGAAATAATAAAAAAAT
ATTTTTATTTAATAAAAACAGTGACTTAATCCGACCCGACCCGAATTATATATATTTTCGGGTCG
GTCCGGTTTTTTTCACCCTAAACCCAAACCCGACCTGAATATCACACTTAAAAAAACCCG
Found at i:8836 original size:37 final size:38
Alignment explanation
Indices: 8736--8828 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
8726 CCCTAAACCC
* *
8736 AAACCCGACCCGATCCGACCCGAATATCACACTTAAAA
1 AAACCCGACCCGAACCGACCCAAATATCACACTTAAAA
*
8774 AAACCCGACCCGACCCGACCCAAATATCACACTT-AAA
1 AAACCCGACCCGAACCGACCCAAATATCACACTTAAAA
8811 AAACCCGACCCGAACCGA
1 AAACCCGACCCGAACCGA
8829 ACAAAATAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 20 0.38
38 32 0.62
ACGTcount: A:0.40, C:0.40, G:0.11, T:0.10
Consensus pattern (38 bp):
AAACCCGACCCGAACCGACCCAAATATCACACTTAAAA
Found at i:11269 original size:31 final size:31
Alignment explanation
Indices: 11234--11303 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
11224 ATTGGACTTT
* * *
11234 AAACTTTTATATAT-ATTTTAATTTCATCCTC
1 AAACTTTTACAT-TCATTTTAAATTAATCCTC
* *
11265 AAACTATGACATTCATTTTAAATTAATCCTC
1 AAACTTTTACATTCATTTTAAATTAATCCTC
11296 AAACTTTT
1 AAACTTTT
11304 TGCGCATTCC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.36, C:0.17, G:0.01, T:0.46
Consensus pattern (31 bp):
AAACTTTTACATTCATTTTAAATTAATCCTC
Found at i:18038 original size:28 final size:27
Alignment explanation
Indices: 18007--18067 Score: 63
Period size: 28 Copynumber: 2.2 Consensus size: 27
17997 TTATGTAATG
18007 AATTTTTTAAATAATTA-TAGTTTAATTT
1 AATTTTTT-AATAATTATTA-TTTAATTT
**
18035 AATTACTTAATAATTATTTATTTAATTT
1 AATTTTTTAATAATTA-TTATTTAATTT
18063 -ATTTT
1 AATTTT
18068 AAAATAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
27 11 0.41
28 14 0.52
29 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (27 bp):
AATTTTTTAATAATTATTATTTAATTT
Found at i:21440 original size:2 final size:2
Alignment explanation
Indices: 21433--21467 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21423 TAGCCATAAG
21433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21468 AAGGTAAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22457 original size:2 final size:2
Alignment explanation
Indices: 22450--22494 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
22440 TGTTTATTTC
22450 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
22492 TA T
1 TA T
22495 GTTGTACGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22882 original size:20 final size:20
Alignment explanation
Indices: 22859--22912 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
22849 AACGCGATTT
* *
22859 AGAAAACCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
22879 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
22899 AGAAAATCGCAACG
1 AGAAAATCGCAACG
22913 CGAGCTTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.52, C:0.20, G:0.19, T:0.09
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:23012 original size:20 final size:20
Alignment explanation
Indices: 22950--23014 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
22940 AGAAGAAAAG
22950 CGCAATGCGATTGATAGAAT
1 CGCAATGCGATTGATAGAAT
* * *
22970 CACAATGCGATTTATAAAAT
1 CGCAATGCGATTGATAGAAT
* *
22990 CGCAATGCGATTGAGAGAGT
1 CGCAATGCGATTGATAGAAT
23010 CGCAA
1 CGCAA
23015 AAAAGATAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (20 bp):
CGCAATGCGATTGATAGAAT
Found at i:23066 original size:6 final size:6
Alignment explanation
Indices: 23055--23099 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
23045 GACACGTATT
23055 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
23100 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:23805 original size:6 final size:6
Alignment explanation
Indices: 23784--23826 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
23774 TCTCGTCTCG
23784 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
23827 AATACGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:23941 original size:20 final size:20
Alignment explanation
Indices: 23916--24046 Score: 145
Period size: 20 Copynumber: 6.4 Consensus size: 20
23906 CTTTTGAACG
23916 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTATAAATCGCA
* * *
23936 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCA
* *
23956 TTGCGATTCTCTTCTAAATCGCG
1 TTGCGA-T-TC-TATAAATCGCA
* * *
23979 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATAAATCGCA
*
23999 TTGCGATTATATAAATCGCA
1 TTGCGATTCTATAAATCGCA
*
24019 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATAAATCGCA
24039 TTGCGATT
1 TTGCGATT
24047 TTCTTCTAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
20 74 0.80
21 3 0.03
22 2 0.02
23 14 0.15
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (20 bp):
TTGCGATTCTATAAATCGCA
Found at i:23960 original size:40 final size:40
Alignment explanation
Indices: 23916--24046 Score: 181
Period size: 40 Copynumber: 3.2 Consensus size: 40
23906 CTTTTGAACG
*
23916 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
* * *
23956 TTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA-T-TC-TATAAATCGCATTGCGATTCTCTCAATCGCA
* *
23999 TTGCGATTATATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
24039 TTGCGATT
1 TTGCGATT
24047 TTCTTCTAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
40 41 0.52
41 2 0.03
42 3 0.04
43 33 0.42
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTATAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:23983 original size:43 final size:42
Alignment explanation
Indices: 23927--24067 Score: 187
Period size: 43 Copynumber: 3.4 Consensus size: 42
23917 TGCGATTCTA
*
23927 TAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTTC
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATT-TCTTC
* * * *
23970 TAAATCGCGTTGCGACTCTCTCAATCGCATTGCGA-TT-ATA
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTCTTC
*
24010 TAAATCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTC
1 TAAATCGCATTGCGATTCTCTCAATCGCATTGCGA-TTTCTTC
*
24053 TAAATCGCGTTGCGA
1 TAAATCGCATTGCGA
24068 ACTTGGAAGC
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 33 0.39
41 1 0.01
42 3 0.04
43 47 0.56
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (42 bp):
TAAATCGCATTGCGATTCTCTCAATCGCATTGCGATTTCTTC
Found at i:24144 original size:20 final size:20
Alignment explanation
Indices: 23914--24171 Score: 126
Period size: 20 Copynumber: 12.6 Consensus size: 20
23904 TTCTTTTGAA
* *
23914 CGTTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
23934 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
23954 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
23977 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
23997 CATTGCGATTATATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
24017 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
24037 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
24060 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
24081 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
24099 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
24121 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
24141 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
24160 CGTTGCGATTTT
1 CGTTGCGATTTT
24172 ATTGGTCATT
Statistics
Matches: 185, Mismatches: 42, Indels: 23
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.01
19 17 0.09
20 118 0.64
21 15 0.08
22 5 0.03
23 28 0.15
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:24161 original size:19 final size:20
Alignment explanation
Indices: 24121--24171 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
24111 TTCTTTTTAA
*
24121 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
24141 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
24160 CGTTGCGATTTT
1 CGTTGCGATTTT
24172 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:24995 original size:27 final size:27
Alignment explanation
Indices: 24957--25010 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
24947 ACAATTAAAT
24957 TCAAAAGACCTTCCACAGAGAGGCCAA
1 TCAAAAGACCTTCCACAGAGAGGCCAA
24984 TCAAAAGACCTTCCACAGAGAGGCCAA
1 TCAAAAGACCTTCCACAGAGAGGCCAA
25011 CAGCAATTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.30, G:0.19, T:0.11
Consensus pattern (27 bp):
TCAAAAGACCTTCCACAGAGAGGCCAA
Found at i:35793 original size:2 final size:2
Alignment explanation
Indices: 35778--35811 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
35768 AATAATAAAA
* *
35778 AT AT AT AC AA 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
35812 TTGGATATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:36123 original size:20 final size:21
Alignment explanation
Indices: 36098--36149 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
36088 TTTTCCCAAT
*
36098 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
36118 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
36139 TCGCAATGCGA
1 TCGCAATGCGA
36150 TAATACAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:36746 original size:19 final size:19
Alignment explanation
Indices: 36708--36774 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
36698 TTCGAGAATG
36708 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
36728 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
36747 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
36766 AAAATCGCA
1 AAAATCGCA
36775 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:36818 original size:20 final size:19
Alignment explanation
Indices: 36770--36935 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
36760 GAAACCAAAA
*
36770 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
36789 TCGCGTTGCGATTTTCAAT
1 TCGCGTTGCGATTTTCATT
36808 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
36828 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
36844 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
36861 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
36875 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
36894 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
36914 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
36934 TC
1 TC
36936 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:36860 original size:33 final size:33
Alignment explanation
Indices: 36823--36910 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
36813 GTTGCGATTT
* *
36823 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
36856 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
36889 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
36911 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:39015 original size:21 final size:21
Alignment explanation
Indices: 38991--39057 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
38981 TCATTCCTCG
38991 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
39012 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
39033 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
39054 AGAG
1 AGAG
39058 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:39015 original size:42 final size:42
Alignment explanation
Indices: 38935--39057 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
38925 GCCCAACTCG
* * ** * * *
38935 CCTATCATCCCTCAAGAGTCTACTCCTATCGTTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
38977 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
* * * * *
39019 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
39058 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
Found at i:40435 original size:14 final size:14
Alignment explanation
Indices: 40416--40451 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
40406 ATTGTTTAAT
40416 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
40430 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
40444 TGATTTGT
1 TGATTTGT
40452 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:40652 original size:19 final size:19
Alignment explanation
Indices: 40630--40780 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
40620 CGAAATTAAA
40630 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
40649 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
40664 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
40682 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
40696 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
40715 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
40730 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * ** *
40748 TTCGCATTGCAATAGTAAT
1 TTCGCGTTGCGATTTTCAT
40767 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
40781 GGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 28 0.30
16 6 0.06
17 6 0.06
19 44 0.47
20 9 0.10
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:40676 original size:33 final size:32
Alignment explanation
Indices: 40634--40757 Score: 187
Period size: 33 Copynumber: 3.8 Consensus size: 32
40624 ATTAAATTCG
40634 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
40667 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
40700 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
40733 CGTTGCGATTTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCATTGC
40758 AATAGTAATT
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:40723 original size:66 final size:66
Alignment explanation
Indices: 40627--40757 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
40617 ACGCGAAATT
*
40627 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
40692 G
66 G
*
40693 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
40758 AATAGTAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:43070 original size:12 final size:12
Alignment explanation
Indices: 43053--43077 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43043 TCTTCGGGGA
43053 CTTTTTCTTCTT
1 CTTTTTCTTCTT
43065 CTTTTTCTTCTT
1 CTTTTTCTTCTT
43077 C
1 C
43078 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:43286 original size:24 final size:24
Alignment explanation
Indices: 43252--43305 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
43242 CTGAAACATC
* *
43252 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
43276 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
43300 ATCAAA
1 ATCAAA
43306 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:44445 original size:14 final size:16
Alignment explanation
Indices: 44425--44498 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
44415 TGAAAATCGC
44425 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
44440 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
44457 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
44476 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
44492 -TTGCGAT
1 ATTGCGAT
44499 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:44462 original size:19 final size:19
Alignment explanation
Indices: 44421--44488 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
44411 GAAATGAAAA
44421 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
44437 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
44454 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
44473 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
44489 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:44464 original size:52 final size:52
Alignment explanation
Indices: 44402--44516 Score: 140
Period size: 52 Copynumber: 2.2 Consensus size: 52
44392 AACGAGAAAA
* ***
44402 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** **
44454 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
44506 TCGCATTGCGA
1 TCGCATTGCGA
44517 TAGTCTGTTT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:44624 original size:14 final size:14
Alignment explanation
Indices: 44605--44641 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
44595 CATCAATTAA
44605 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
44619 ACAAATCATCTTTT
1 ACAAATCAACATTT
44633 ACAAATCAA
1 ACAAATCAA
44642 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:46551 original size:19 final size:18
Alignment explanation
Indices: 46529--46586 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 18
46519 AGAAATGGCT
46529 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
46548 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
46562 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
46580 ATCGCAA
1 ATCGCAA
46587 CGACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 10 0.31
19 7 0.22
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:46564 original size:14 final size:14
Alignment explanation
Indices: 46545--46602 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
46535 ATGCGAAATG
46545 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
46559 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
46575 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
46591 AAAATCGCAACG
1 AAAATCGCAACG
46603 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:46587 original size:32 final size:33
Alignment explanation
Indices: 46529--46607 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
46519 AGAAATGGCT
*
46529 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
46562 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
46594 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
46608 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:46636 original size:19 final size:19
Alignment explanation
Indices: 46614--46695 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
46604 GAAACACAAA
*
46614 TCGCATAGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
46633 TCGCGTTGCGATTTT-A--
1 TCGCATTGCGATTTTCATT
*
46649 TCG--TTACGA-TTTCATT
1 TCGCATTGCGATTTTCATT
46665 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
46684 TCGCATTGCGAT
1 TCGCATTGCGAT
46696 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
13 3 0.06
14 6 0.11
16 6 0.11
18 6 0.11
19 32 0.60
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:46702 original size:19 final size:19
Alignment explanation
Indices: 46660--46723 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
46650 CGTTACGATT
**
46660 TCATTTCGCATTGCGATTT
1 TCATTTCGCATTGCGATAG
46679 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
* *
46698 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCATTGCGATAG
46718 TCATTT
1 TCATTT
46724 TCGTGTTGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:46732 original size:20 final size:20
Alignment explanation
Indices: 46680--46723 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
46670 TTGCGATTTT
*
46680 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
46699 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
46719 CATTT
1 CATTT
46724 TCGTGTTGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:47236 original size:18 final size:18
Alignment explanation
Indices: 47210--47254 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
47200 GTCGATCAGA
47210 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
*
47228 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
47246 TGATGGCTC
1 TGATGGCTC
47255 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGG
Found at i:48599 original size:20 final size:20
Alignment explanation
Indices: 48574--48611 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48564 AATAGTTTCT
48574 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
48594 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
48612 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:48902 original size:22 final size:22
Alignment explanation
Indices: 48875--48918 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
48865 GATGGAGATA
48875 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
48897 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
48919 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:49128 original size:20 final size:20
Alignment explanation
Indices: 49103--49155 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
49093 TGCGATTTAT
*
49103 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
*
49123 TATCGCATTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
49143 TATCTCGTTGCGA
1 TATCGCGTTGCGA
49156 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:49173 original size:41 final size:41
Alignment explanation
Indices: 49123--49200 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
49113 CGAAAGTCAG
* *
49123 TATCGCATTGCGAA-AGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGC-AATAGTAAGTATCGCATTGCGATTTTTTAT
*
49164 TATCGCATTGCAATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCAATAGTAAGTATCGCATTGCGATTTT
49201 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 31 0.94
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCAATAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:49215 original size:21 final size:21
Alignment explanation
Indices: 49186--49278 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
49176 ATAGTCAGTA
49186 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
49207 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
49227 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * * **
49248 TTGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
49268 TCGCATTGCGA
1 TCGCATTGCGA
49279 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:49231 original size:41 final size:41
Alignment explanation
Indices: 49186--49278 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
49176 ATAGTCAGTA
49186 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
49227 TCGCATTGCGATTTTCCCAATTTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
49268 TCGCATTGCGA
1 TCGCATTGCGA
49279 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:50192 original size:9 final size:9
Alignment explanation
Indices: 50180--50231 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
50170 TAATTTTTTG
50180 TATTTAATT
1 TATTTAATT
*
50189 TATTTAA-G
1 TATTTAATT
50197 TATTTAATT
1 TATTTAATT
50206 TATTTAA--
1 TATTTAATT
* *
50213 TATTTTACT
1 TATTTAATT
50222 TATTTAATT
1 TATTTAATT
50231 T
1 T
50232 TTTTGCAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 6 0.17
8 7 0.20
9 22 0.63
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (9 bp):
TATTTAATT
Found at i:50201 original size:17 final size:17
Alignment explanation
Indices: 50168--50228 Score: 76
Period size: 17 Copynumber: 3.8 Consensus size: 17
50158 TTATTATATT
50168 TTTAATTT-TTT--GTA
1 TTTAATTTATTTAAGTA
50182 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAAGTA
50199 TTTAATTTATTTAA-TA
1 TTTAATTTATTTAAGTA
* *
50215 TTTTACTTATTTAA
1 TTTAATTTATTTAA
50229 TTTTTTTGCA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.19
15 3 0.07
16 14 0.33
17 17 0.40
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTAATTTATTTAAGTA
Found at i:50217 original size:33 final size:31
Alignment explanation
Indices: 50168--50228 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
50158 TTATTATATT
* *
50168 TTTAATTTTTTGTATTTAATTTATTTAAGTA
1 TTTAATTTTTTATATTTAACTTATTTAAGTA
*
50199 TTTAATTTATTTAATATTTTACTTATTTAA
1 TTTAATTT-TTT-ATATTTAACTTATTTAA
50229 TTTTTTTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 8 0.32
32 3 0.12
33 14 0.56
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (31 bp):
TTTAATTTTTTATATTTAACTTATTTAAGTA
Found at i:50224 original size:16 final size:16
Alignment explanation
Indices: 50188--50233 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
50178 TGTATTTAAT
* *
50188 TTATTTAAGTATTTAAT
1 TTATTTAA-TATTTTAC
50205 TTATTTAATATTTTAC
1 TTATTTAATATTTTAC
50221 TTATTTAAT-TTTT
1 TTATTTAATATTTT
50234 TTGCAGATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTATTTAATATTTTAC
Found at i:54022 original size:21 final size:22
Alignment explanation
Indices: 53996--54039 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
53986 CAGTGTCTCC
*
53996 TAGAAAATTGTTTTC-AAATTT
1 TAGAAAATTATTTTCAAAATTT
54017 TAGAAAATTATTTTCAAAATTT
1 TAGAAAATTATTTTCAAAATTT
54039 T
1 T
54040 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (22 bp):
TAGAAAATTATTTTCAAAATTT
Found at i:55138 original size:20 final size:20
Alignment explanation
Indices: 55115--55237 Score: 56
Period size: 21 Copynumber: 6.0 Consensus size: 20
55105 TTCGCAACGT
55115 GATTATGACAATCGCAATGC
1 GATTATGACAATCGCAATGC
** **
55135 GATT-TTCCAATTTCGCGTTGC
1 GATTATGACAA--TCGCAATGC
* **
55156 GATTTTCCCAATTCGCAATGC
1 GATTATGACAA-TCGCAATGC
* *
55177 GAATAAGTA-AATCGCAATGC
1 GATTATG-ACAATCGCAATGC
*
55197 GAATT-TAGAAAATCGCAATGC
1 G-ATTAT-GACAATCGCAATGC
*
55218 GA-TACTGACTATCGCAATGC
1 GATTA-TGACAATCGCAATGC
55238 AATTTTCTTA
Statistics
Matches: 78, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
19 5 0.06
20 28 0.36
21 40 0.51
22 5 0.06
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (20 bp):
GATTATGACAATCGCAATGC
Found at i:55177 original size:21 final size:21
Alignment explanation
Indices: 55126--55178 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
55116 ATTATGACAA
55126 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
55147 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
55168 TCGCAATGCGA
1 TCGCAATGCGA
55179 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:55211 original size:21 final size:20
Alignment explanation
Indices: 55168--55219 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
55158 TTTTCCCAAT
*
55168 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
*
55188 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAA-TAAGAAAA
55209 TCGCAATGCGA
1 TCGCAATGCGA
55220 TACTGACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:55263 original size:21 final size:21
Alignment explanation
Indices: 55229--55291 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
55219 ATACTGACTA
* * *
55229 TCGCAATGCAATTTTCTTAAT
1 TCGCATTGCGATTTTCATAAT
* *
55250 TCGCATTGCGATTTACGT-AT
1 TCGCATTGCGATTTTCATAAT
* *
55270 TTGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
55291 T
1 T
55292 AGCAATGTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:55352 original size:21 final size:21
Alignment explanation
Indices: 55293--55384 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 21
55283 TTCATAATTA
* *
55293 GCAATGTGAA-TACGTAAATC
1 GCAATGCGAATTAAGTAAATC
*
55313 GCAACGCG-ATTAAGTAAATC
1 GCAATGCGAATTAAGTAAATC
* *
55333 GCAATGCGAATTAGGAAAATC
1 GCAATGCGAATTAAGTAAATC
** * *
55354 AAAATGC-AAATACGTAAATC
1 GCAATGCGAATTAAGTAAATC
*
55374 GCAATTCGAAT
1 GCAATGCGAAT
55385 CTTACTATCG
Statistics
Matches: 54, Mismatches: 15, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.02
20 36 0.67
21 17 0.31
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.22
Consensus pattern (21 bp):
GCAATGCGAATTAAGTAAATC
Found at i:55628 original size:41 final size:41
Alignment explanation
Indices: 55586--55723 Score: 197
Period size: 41 Copynumber: 3.4 Consensus size: 41
55576 TGCGTTGCAT
*
55586 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAG
55627 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAG
* * ** ** *
55668 TTCGCGTTGCAAT-TTTCCAGTTCGCATTGCGATTTTCCAG
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAG
55708 TTCGCGTTGCGATAGT
1 TTCGCGTTGCGATAGT
55724 CTACAGTTGT
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 33 0.38
41 53 0.62
ACGTcount: A:0.17, C:0.21, G:0.25, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAG
Found at i:55633 original size:20 final size:20
Alignment explanation
Indices: 55608--55767 Score: 146
Period size: 20 Copynumber: 7.9 Consensus size: 20
55598 TAGTTGAAAA
*
55608 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
* ** **
55628 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCAGT
55649 TCGCGTTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
*
55669 TCGCGTTGCAATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
*
55689 TCGCATTGCGATTTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
* *
55709 TCGCGTTGCGATAGTCTACAGT
1 TCGCGTTGCGAT--TTTCCAGT
* *
55731 T-GTCGTTGTGATTTTCCAAAT
1 TCG-CGTTGCGATTTTCC-AGT
55752 T--CGTTGCGATTTTCCA
1 TCGCGTTGCGATTTTCCA
55768 AATTCGTTGC
Statistics
Matches: 114, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
18 1 0.01
19 13 0.11
20 66 0.58
21 19 0.17
22 15 0.13
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:55757 original size:19 final size:19
Alignment explanation
Indices: 55733--55779 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
55723 TCTACAGTTG
*
55733 TCGTTGTGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
55752 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
55771 TCGTTGCGA
1 TCGTTGCGA
55780 AAATTCGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:55757 original size:81 final size:80
Alignment explanation
Indices: 55608--55767 Score: 198
Period size: 81 Copynumber: 2.0 Consensus size: 80
55598 TAGTTGAAAA
* * *
55608 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAGTTCGC
1 TCGCATTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-C
55673 GTTGCAATTTTCCAGT
65 GTTGCAATTTTCCAGT
* * * *
55689 TCGCATTGCGATTTTCCAGTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGTGATTTTCCAAATT
1 TCGCATTGCGATTTTCCAGTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATT
*
55753 -CGTTGCGATTTTCCA
63 CCGTTGCAATTTTCCA
55768 AATTCGTTGC
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
81 51 0.75
82 14 0.21
83 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (80 bp):
TCGCATTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCG
TTGCAATTTTCCAGT
Found at i:55785 original size:13 final size:13
Alignment explanation
Indices: 55767--55792 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55757 GCGATTTTCC
55767 AAATTCGTTGCGA
1 AAATTCGTTGCGA
55780 AAATTCGTTGCGA
1 AAATTCGTTGCGA
55793 TAGTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
AAATTCGTTGCGA
Found at i:56517 original size:22 final size:22
Alignment explanation
Indices: 56492--56548 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
56482 CTTTTTTTTA
* *
56492 ACTATCACAACGACAACTGTAG
1 ACTATCGCAACAACAACTGTAG
56514 ACTATCGCAACAACAACTGTAG
1 ACTATCGCAACAACAACTGTAG
56536 ACTATCGCAACAA
1 ACTATCGCAACAA
56549 ATTTGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.42, C:0.28, G:0.12, T:0.18
Consensus pattern (22 bp):
ACTATCGCAACAACAACTGTAG
Found at i:56585 original size:19 final size:19
Alignment explanation
Indices: 56539--56586 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
56529 ACTGTAGACT
*
56539 ATCGCAACAAATTTGAAAA
1 ATCGCAACGAATTTGAAAA
*
56558 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGAAAA
56577 ATCGCAACGA
1 ATCGCAACGA
56587 CAACTGTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (19 bp):
ATCGCAACGAATTTGAAAA
Found at i:56624 original size:20 final size:20
Alignment explanation
Indices: 56599--56650 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
56589 ACTGTAGACT
56599 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
56619 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
56639 ATCGCAATGCGA
1 ATCGCAACGCGA
56651 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:57369 original size:19 final size:19
Alignment explanation
Indices: 57345--57389 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
57335 GCAACGAGAG
**
57345 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
57364 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
57383 AATCGCA
1 AATCGCA
57390 TTGTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:57407 original size:19 final size:20
Alignment explanation
Indices: 57385--57502 Score: 88
Period size: 19 Copynumber: 6.7 Consensus size: 20
57375 GAAACCAAAA
*
57385 TCGC-ATTGTGATTTTCATT
1 TCGCGATTGCGATTTTCATT
*
57404 TCGCGGTTGCGATTTTCATT
1 TCGCGATTGCGATTTTCATT
57424 TCGCG-TTGCGA--TTC---
1 TCGCGATTGCGATTTTCATT
*
57438 TCTCG-TTGCGATTTTCATT
1 TCGCGATTGCGATTTTCATT
57457 TCGCG-TTGCGA--TTC---
1 TCGCGATTGCGATTTTCATT
*
57471 TCTCG-TTGCGATTTTCATT
1 TCGCGATTGCGATTTTCATT
57490 TCGCG-TTGCGATT
1 TCGCGATTGCGATT
57503 CTCTCGTTGC
Statistics
Matches: 82, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
14 20 0.24
16 6 0.07
17 6 0.07
19 32 0.39
20 18 0.22
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (20 bp):
TCGCGATTGCGATTTTCATT
Found at i:57446 original size:14 final size:14
Alignment explanation
Indices: 57427--57548 Score: 82
Period size: 14 Copynumber: 7.6 Consensus size: 14
57417 TTTCATTTCG
57427 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
57441 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
57460 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
57474 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
57493 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
57507 CGTTGCGATAGTCATTTCA
1 CGTTGCGAT--TC---TCT
57526 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
57540 CGTTGCGAT
1 CGTTGCGAT
57549 AGTTATTTTC
Statistics
Matches: 87, Mismatches: 6, Indels: 30
0.71 0.05 0.24
Matches are distributed among these distances:
14 40 0.46
16 8 0.09
17 8 0.09
19 31 0.36
ACGTcount: A:0.11, C:0.25, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:57451 original size:33 final size:33
Alignment explanation
Indices: 57409--57597 Score: 263
Period size: 33 Copynumber: 5.5 Consensus size: 33
57399 TCATTTCGCG
57409 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
57442 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
57475 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
** *
57508 GTTGCGATAGTCATTTCACGTTGCGATTCTCTC
1 GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
*
57541 GTTGCGATAGTT-ATTTTCGCGTTGCGATTTTCATTATCTC
1 GTTGCGAT-TTTCA-TTTCGCGTTGCGA--TTC----TCTC
57581 GTTGCGATTTTCATTTC
1 GTTGCGATTTTCATTTC
57598 AAACAAAAGA
Statistics
Matches: 140, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
33 105 0.75
34 13 0.09
36 3 0.02
39 6 0.04
40 13 0.09
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.46
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTCTCTC
Found at i:58904 original size:21 final size:21
Alignment explanation
Indices: 58880--58947 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
58870 CCAGAGCCAT
58880 CACCTGATCGACCCGACTATA
1 CACCTGATCGACCCGACTATA
* * ** *
58901 CACCT-CTACAACGAGAGCCAT-
1 CACCTGAT-CGACCCGA-CTATA
58922 CACCTGATCGACCCGACTATA
1 CACCTGATCGACCCGACTATA
58943 CACCT
1 CACCT
58948 CTACAACGAG
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.29, C:0.40, G:0.13, T:0.18
Consensus pattern (21 bp):
CACCTGATCGACCCGACTATA
Found at i:58931 original size:42 final size:42
Alignment explanation
Indices: 58872--58968 Score: 194
Period size: 42 Copynumber: 2.3 Consensus size: 42
58862 CACTTCACCC
58872 AGAGCCATCACCTGATCGACCCGACTATACACCTCTACAACG
1 AGAGCCATCACCTGATCGACCCGACTATACACCTCTACAACG
58914 AGAGCCATCACCTGATCGACCCGACTATACACCTCTACAACG
1 AGAGCCATCACCTGATCGACCCGACTATACACCTCTACAACG
58956 AGAGCCATCACCT
1 AGAGCCATCACCT
58969 ATCCCGTCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.31, C:0.38, G:0.14, T:0.16
Consensus pattern (42 bp):
AGAGCCATCACCTGATCGACCCGACTATACACCTCTACAACG
Found at i:58967 original size:21 final size:21
Alignment explanation
Indices: 58901--58968 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
58891 CCCGACTATA
58901 CACCTCTACAACGAGAGCCAT
1 CACCTCTACAACGAGAGCCAT
* * ** *
58922 CACCT-GATCGACCCGA-CTAT
1 CACCTCTA-CAACGAGAGCCAT
58942 ACACCTCTACAACGAGAGCCAT
1 -CACCTCTACAACGAGAGCCAT
58964 CACCT
1 CACCT
58969 ATCCCGTCAA
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 4 0.12
21 25 0.76
22 4 0.12
ACGTcount: A:0.31, C:0.40, G:0.13, T:0.16
Consensus pattern (21 bp):
CACCTCTACAACGAGAGCCAT
Found at i:59694 original size:21 final size:21
Alignment explanation
Indices: 59670--59736 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
59660 TCATTCCTCG
59670 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
59691 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
59712 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
59733 AGAG
1 AGAG
59737 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:59694 original size:42 final size:42
Alignment explanation
Indices: 59643--59736 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
59633 CCACTCATAT
* *
59643 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
59685 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
59727 CATTCAAGAG
1 CGTTCAAGAG
59737 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:61107 original size:14 final size:14
Alignment explanation
Indices: 61088--61123 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
61078 ATTGTTTAAT
61088 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
61102 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
61116 TGATTTGT
1 TGATTTGT
61124 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:61202 original size:27 final size:27
Alignment explanation
Indices: 61164--61223 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
61154 GCTTGTTTAA
*
61164 TTGATTGAAATGTAATGGTTGATTTTG
1 TTGATTGAAATGTAATGGTTAATTTTG
61191 TTGATTGAAATGTAATGGTTAATTTTG
1 TTGATTGAAATGTAATGGTTAATTTTG
61218 TTGATT
1 TTGATT
61224 TCAATCTGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (27 bp):
TTGATTGAAATGTAATGGTTAATTTTG
Found at i:61279 original size:19 final size:19
Alignment explanation
Indices: 61257--61315 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
61247 AAAAATTACT
61257 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
61276 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
61290 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
61309 ATCGCAA
1 ATCGCAA
61316 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:61299 original size:33 final size:33
Alignment explanation
Indices: 61257--61349 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
61247 AAAAATTACT
* *
61257 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
61290 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
61323 ATCGCAACGCGAAACT-AAAATCGCAAC
1 ATCGCAATGCGAAA-TGAAAATCGCAAC
61350 ACGAAACTAA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 55 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:61344 original size:19 final size:19
Alignment explanation
Indices: 61289--61365 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
61279 GCAACGAGAG
*
61289 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
61308 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
61322 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
61341 AATCGCAACACGAAACTAA
1 AATCGCAACGCGAAACTAA
*
61360 ATTCGC
1 AATCGC
61366 GTTGTGATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 33 0.66
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:61408 original size:33 final size:33
Alignment explanation
Indices: 61365--61491 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
61355 ACTAAATTCG
* * *
61365 CGTTGTGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
61398 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
61431 CGTTGCGATTTTCATTTCGTATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
61464 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
61492 AGTAATTTCT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:61424 original size:19 final size:18
Alignment explanation
Indices: 61400--61491 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
61390 GATTCCCTCG
61400 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
*
61419 TTGCGA--TTC-TCTCG-
1 TTGCGATTTTCATTTCGA
61433 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCG-A
*
61452 TTGCGA--TT-ATCTCG-
1 TTGCGATTTTCATTTCGA
61466 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCG-A
61485 TTGCGAT
1 TTGCGAT
61492 AGTAATTTCT
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 12 0.20
16 14 0.24
17 14 0.24
19 19 0.32
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGA
Found at i:61438 original size:14 final size:14
Alignment explanation
Indices: 61386--61473 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
61376 TCATTTCGCT
*
61386 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
61400 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
61417 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
61433 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
61450 TATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
61466 TTGCGATT
1 TTGCGATT
61474 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:64039 original size:24 final size:24
Alignment explanation
Indices: 64005--64058 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
63995 CTGAAACATC
*
64005 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
64029 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
64053 ATCAAA
1 ATCAAA
64059 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:64827 original size:20 final size:20
Alignment explanation
Indices: 64778--64829 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
64768 TTGCGAACTT
64778 TGAAAATCGCAACGAGATTC
1 TGAAAATCGCAACGAGATTC
***
64798 TGACTTTCGCAACGAGATTC
1 TGAAAATCGCAACGAGATTC
64818 TGAAAATCGCAA
1 TGAAAATCGCAA
64830 TCATCTTCAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
TGAAAATCGCAACGAGATTC
Found at i:65068 original size:20 final size:20
Alignment explanation
Indices: 65043--65096 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
65033 CAACGGGTAA
65043 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
65063 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* *
65083 ATAGCAATGCGAAA
1 ATCGCAACGCGAAA
65097 TGAAAATGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:65138 original size:19 final size:19
Alignment explanation
Indices: 65116--65164 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
65106 GATTTTCTCG
*
65116 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCACA
65135 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCACA
65154 TTGCGATTTTC
1 TTGCGATTTTC
65165 TCGTTGCGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.16, C:0.20, G:0.14, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:66799 original size:41 final size:42
Alignment explanation
Indices: 66745--66836 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
66735 CCTCTTCAAC
* *
66745 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* *
66786 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
66828 GATGACAGG
1 GATGACAGG
66837 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 20 0.44
42 25 0.56
ACGTcount: A:0.21, C:0.15, G:0.42, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:66801 original size:21 final size:21
Alignment explanation
Indices: 66772--66832 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
66762 GAACGGTGGG
*
66772 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
66793 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
66814 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
66833 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:67199 original size:20 final size:20
Alignment explanation
Indices: 67174--67246 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
67164 GAAGAATAGT
*
67174 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAA
*
67194 TTACTTTCGCAACGCGAAAA
1 TTACTTTCGCAACACGAAAA
* * * *
67214 TGACTATCGCAACGCGGAAA
1 TTACTTTCGCAACACGAAAA
* *
67234 TGACTATCGCAAC
1 TTACTTTCGCAAC
67247 GCGGAAATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAA
Found at i:67224 original size:40 final size:40
Alignment explanation
Indices: 67180--67265 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
67170 TAGTTTACTT
* *
67180 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* * *
67220 TCGCAACGCGGAAATGACTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
67260 TCGCAA
1 TCGCAA
67266 TGCGAAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:67247 original size:20 final size:20
Alignment explanation
Indices: 67200--67286 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
67190 AAACTTACTT
*
67200 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
67220 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
67240 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
67260 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
67279 TCGCAACG
1 TCGCAACG
67287 AAAAAATCGC
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 14 0.23
20 46 0.77
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:67334 original size:19 final size:18
Alignment explanation
Indices: 67312--67404 Score: 76
Period size: 19 Copynumber: 5.4 Consensus size: 18
67302 GAAACACAAA
67312 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
* *
67331 TCGCGTTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
67347 TCG--TTGCGATTTTTATT
1 TCGCATTGCGA-TTTTATT
*
67364 TCGCATTGCGA-TTT-TG
1 TCGCATTGCGATTTTATT
67380 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTT-ATT
67397 TCGCATTG
1 TCGCATTG
67405 TGATAGCCAT
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 12 0.20
15 3 0.05
16 11 0.19
17 11 0.19
18 3 0.05
19 19 0.32
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (18 bp):
TCGCATTGCGATTTTATT
Found at i:67353 original size:14 final size:14
Alignment explanation
Indices: 67334--67392 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
67324 TTTCATTTCG
67334 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
67348 CGTTGCGATTTTTATTT
1 CGTTGCGA--TTT-TGT
67365 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
67381 CGTTGCGATTTT
1 CGTTGCGATTTT
67393 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
16 7 0.18
17 7 0.18
19 6 0.16
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:67359 original size:33 final size:33
Alignment explanation
Indices: 67317--67404 Score: 158
Period size: 33 Copynumber: 2.7 Consensus size: 33
67307 ACAAATCGCA
*
67317 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
67350 TTGCGATTTTTATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
67383 TTGCGATTTTCATTTCGCATTG
1 TTGCGATTTTCATTTCGCATTG
67405 TGATAGCCAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:67435 original size:20 final size:19
Alignment explanation
Indices: 67381--67436 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
67371 GCGATTTTGT
**
67381 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* * *
67400 CATTGTGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
67420 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
67437 TCGTGTTGCA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:67993 original size:18 final size:18
Alignment explanation
Indices: 67970--68017 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
67960 CGGGTCGATC
67970 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
67988 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
68006 AGGTGATGGCTC
1 AGGTGATGGCTC
68018 CCTAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:69385 original size:20 final size:20
Alignment explanation
Indices: 69337--69393 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
69327 AATAGTTTCT
*
69337 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACAC
*
69357 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACAC
** *
69377 GAATTTGACTATCGCAA
1 GAAAATGACAATCGCAA
69394 TGAGAGAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGACAATCGCAACAC
Found at i:69687 original size:22 final size:22
Alignment explanation
Indices: 69660--69725 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
69650 GATGGAGATA
69660 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
69682 GACGGATTTCGCCGGAGATGAG
1 GACGGATTTCGCCGGAGATGGG
**
69704 GACGGATTTCGTTGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
69726 TGAGAGAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.20, C:0.15, G:0.44, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:70011 original size:41 final size:41
Alignment explanation
Indices: 69898--70029 Score: 158
Period size: 41 Copynumber: 3.2 Consensus size: 41
69888 GAAAATTGCA
* * * * *
69898 TTGCGATTATGTATTATCTCATTGCGAAAGTCAGTATTGAG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
** * * *
69939 TTGCGAAATT-AAGTATCGAGTTGCGAAAGTCAGTATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
*
69979 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCG
1 TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
70020 TTGCGATTTT
1 TTGCGATTTT
70030 CCAAATTCGC
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
40 31 0.42
41 43 0.58
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.37
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGTATCGCG
Found at i:70026 original size:20 final size:20
Alignment explanation
Indices: 69919--70025 Score: 108
Period size: 20 Copynumber: 5.3 Consensus size: 20
69909 TATTATCTCA
* *
69919 TTGCGAAAGTCAGTATTGAG
1 TTGCGAAAGTCAGTATCGCG
* * *
69939 TTGCGAAATTAAGTATCGAG
1 TTGCGAAAGTCAGTATCGCG
69959 TTGCGAAAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
** *
69979 TTGCGATTTTGT-ATTATCGCG
1 TTGCGA--AAGTCAGTATCGCG
*
70000 TTGCGATAGTCAGTATCGCG
1 TTGCGAAAGTCAGTATCGCG
70020 TTGCGA
1 TTGCGA
70026 TTTTCCAAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.04
20 54 0.74
21 14 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (20 bp):
TTGCGAAAGTCAGTATCGCG
Found at i:70044 original size:21 final size:20
Alignment explanation
Indices: 70015--70066 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
70005 ATAGTCAGTA
* *
70015 TCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
**
70036 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
70056 TCGCATTGCGA
1 TCGCATTGCGA
70067 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:70045 original size:41 final size:41
Alignment explanation
Indices: 69912--70047 Score: 125
Period size: 41 Copynumber: 3.3 Consensus size: 41
69902 GATTATGTAT
* * * * ** *
69912 TATCTCATTGCGAAAGTCAGTATTGAGTTGCGAAATT-AAG
1 TATCGCATTGCGATAGTCAGTATCGCGTTGCGATTTTCAAA
* ** *
69952 TATCG-AGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTAT
1 TATCGCA-TTGCGATAGTCAGTATCGCGTTGCGATTTTCAAA
*
69993 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAA
1 TATCGCATTGCGATAGTCAGTATCGCGTTGCGATTTT-CAAA
70035 T-TCGCATTGCGAT
1 TATCGCATTGCGAT
70048 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
39 1 0.01
40 30 0.38
41 46 0.58
42 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (41 bp):
TATCGCATTGCGATAGTCAGTATCGCGTTGCGATTTTCAAA
Found at i:72111 original size:27 final size:27
Alignment explanation
Indices: 72054--72115 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
72044 TAGGGCTTGG
*
72054 GGGTATTTTAGGTTATTTCACACTTAT
1 GGGTATTTTAGGTTATTTCACACTTAA
* *
72081 GGGTATTTT-GGTTATTTTACAGTTGAA
1 GGGTATTTTAGGTTATTTCACACTT-AA
72108 GGGTATTT
1 GGGTATTT
72116 CAATCTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 13 0.42
27 18 0.58
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.48
Consensus pattern (27 bp):
GGGTATTTTAGGTTATTTCACACTTAA
Found at i:74249 original size:20 final size:20
Alignment explanation
Indices: 74226--74293 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
74216 GCAACACAGA
74226 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
74246 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
74266 AGTCAAATTCGCAACACGAA
1 AGTCAAATTCGCAACGCGAT
74286 AGTCAAAT
1 AGTCAAAT
74294 GTTTTTATGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:74260 original size:40 final size:39
Alignment explanation
Indices: 74211--74293 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 39
74201 ATGGATTTGT
* *
74211 AAATTGCAACACAGA-AGTCAAATTCGCAACGCGATAGTC
1 AAATTGCAACAC-GATAGTCAAATTCGCAACACGAAAGTC
*
74250 AAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGTC
1 AAATT-GCAACACGATAGTCAAATTCGCAACACGAAAGTC
74290 AAAT
1 AAAT
74294 GTTTTTATGC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 7 0.18
40 32 0.82
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (39 bp):
AAATTGCAACACGATAGTCAAATTCGCAACACGAAAGTC
Found at i:75284 original size:20 final size:20
Alignment explanation
Indices: 75259--75298 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
75249 TTGAGGATAC
*
75259 TTGCGAATTTGACTTTCGCA
1 TTGCGAATTTGACTATCGCA
75279 TTGCGAATTTGACTATCGCA
1 TTGCGAATTTGACTATCGCA
75299 ACACTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCA
Found at i:75331 original size:20 final size:20
Alignment explanation
Indices: 75306--75355 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
75296 GCAACACTTA
75306 TTTTGCGTTGTGAATTTGAC
1 TTTTGCGTTGTGAATTTGAC
75326 TTTTGCGTTGTGAATTTGAC
1 TTTTGCGTTGTGAATTTGAC
*
75346 TTTCGCGTTG
1 TTTTGCGTTG
75356 ATCGCAACAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.12, G:0.26, T:0.50
Consensus pattern (20 bp):
TTTTGCGTTGTGAATTTGAC
Found at i:75585 original size:39 final size:39
Alignment explanation
Indices: 75531--75617 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
75521 TCAATTTATA
75531 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
75570 GATTTTGATTTCCTTTTGCTTGGCACCATCTGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
75609 GATTTTGAT
1 GATTTTGAT
75618 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:75949 original size:18 final size:18
Alignment explanation
Indices: 75926--75962 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
75916 CTAAATTTAT
75926 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
75944 ATTGAAATTGAAATTCAA
1 ATTGAAATTCAAACTCAA
75962 A
1 A
75963 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:76376 original size:25 final size:25
Alignment explanation
Indices: 76339--76387 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
76329 TTATTTTTCT
* *
76339 AAATAATGTACCCATAACAATGTTC
1 AAATAATGCACCCACAACAATGTTC
*
76364 AAATAATGCACCCACAATAATGTT
1 AAATAATGCACCCACAACAATGTT
76388 TAATTGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.45, C:0.20, G:0.08, T:0.27
Consensus pattern (25 bp):
AAATAATGCACCCACAACAATGTTC
Found at i:76471 original size:20 final size:20
Alignment explanation
Indices: 76448--76489 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
76438 AAACCTGTTG
*
76448 AAGGTAAATTCGCAACGTGA
1 AAGGTAAATTCGCAACGCGA
76468 AAGGTAAATTCGCAACGCGA
1 AAGGTAAATTCGCAACGCGA
76488 AA
1 AA
76490 TAAGCGTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.17
Consensus pattern (20 bp):
AAGGTAAATTCGCAACGCGA
Found at i:76521 original size:20 final size:20
Alignment explanation
Indices: 76498--76559 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
76488 AATAAGCGTT
76498 GCGATAGTCAAATTCGCAAC
1 GCGATAGTCAAATTCGCAAC
* *
76518 GCGAAAGTCAAATTCGCTAC
1 GCGATAGTCAAATTCGCAAC
*
76538 GCGATAGTCAAATTTGCAAC
1 GCGATAGTCAAATTCGCAAC
76558 GC
1 GC
76560 TTATTTCGCG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCAAC
Found at i:79211 original size:24 final size:24
Alignment explanation
Indices: 79177--79230 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
79167 TAATCACATC
79177 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
79201 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
79225 ATCAAA
1 ATCAAA
79231 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:79244 original size:24 final size:24
Alignment explanation
Indices: 79177--79244 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
79167 TAATCACATC
* * *
79177 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
79201 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
79225 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
79245 TAGTACTTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:84335 original size:14 final size:14
Alignment explanation
Indices: 84316--84381 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
84306 TTTAAAATAA
84316 TTATAATAATATAT
1 TTATAATAATATAT
* *
84330 TTATAATTATTTAT
1 TTATAATAATATAT
** **
84344 TATATTTTAATA-GG
1 T-TATAATAATATAT
*
84358 TTAGAATAATATAT
1 TTATAATAATATAT
84372 TTATAATAAT
1 TTATAATAAT
84382 TTTATATTTT
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
13 7 0.19
14 23 0.64
15 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (14 bp):
TTATAATAATATAT
Found at i:84622 original size:10 final size:10
Alignment explanation
Indices: 84607--84634 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
84597 CACCCGAATT
84607 CGACCCGAAC
1 CGACCCGAAC
84617 CGACCCGAAC
1 CGACCCGAAC
84627 CGACCCGA
1 CGACCCGA
84635 TCTCCCCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.50, G:0.21, T:0.00
Consensus pattern (10 bp):
CGACCCGAAC
Found at i:85247 original size:13 final size:13
Alignment explanation
Indices: 85229--85254 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
85219 CAGATCATAT
85229 TATATACATATAC
1 TATATACATATAC
85242 TATATACATATAC
1 TATATACATATAC
85255 CCAAATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.38
Consensus pattern (13 bp):
TATATACATATAC
Found at i:87523 original size:17 final size:18
Alignment explanation
Indices: 87503--87536 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
87493 ATTATATTTA
87503 AAATTGAA-TTTGTTTTG
1 AAATTGAATTTTGTTTTG
87520 AAATTGAATTTTGTTTT
1 AAATTGAATTTTGTTTT
87537 AATTATTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (18 bp):
AAATTGAATTTTGTTTTG
Done.