Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010403.1 Corchorus capsularis cultivar CVL-1 contig10424, 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: 82400
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:3589 original size:42 final size:40
Alignment explanation
Indices: 3535--3649 Score: 135
Period size: 39 Copynumber: 2.8 Consensus size: 40
3525 CTCTCTCCCC
* *
3535 AAAGTCCCCAAACACATATAACACAGGGGCAATTCTCCTTCT
1 AAAGT-CCCAAACACATATAACACAGGGGCAATTCT-ATACT
*
3577 AAAGTCCTCAAACACATATAACACAGAGGC-A-TCTATACT
1 AAAGTCC-CAAACACATATAACACAGGGGCAATTCTATACT
* *
3616 AAAGTCCCTAAACACATGTAACACAAGGGCAATT
1 AAAGTCCC-AAACACATATAACACAGGGGCAATT
3650 TTCTCTACAT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
38 1 0.02
39 28 0.44
40 4 0.06
41 4 0.06
42 26 0.41
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (40 bp):
AAAGTCCCAAACACATATAACACAGGGGCAATTCTATACT
Found at i:5807 original size:40 final size:40
Alignment explanation
Indices: 5752--5828 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
5742 CTCCAACTTC
* *
5752 CTGCTGTAAAAGTCGAC-GTTCTTTTCAATCAATGGGTTTT
1 CTGCTGCAAAAGTCGACGGTTC-TCTCAATCAATGGGTTTT
*
5792 CTGCTGCAGAAGTCGACGGTTCTCTCAATCAATGGGT
1 CTGCTGCAAAAGTCGACGGTTCTCTCAATCAATGGGT
5829 GGTAGAGAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (40 bp):
CTGCTGCAAAAGTCGACGGTTCTCTCAATCAATGGGTTTT
Found at i:6703 original size:26 final size:26
Alignment explanation
Indices: 6667--6886 Score: 130
Period size: 26 Copynumber: 7.8 Consensus size: 26
6657 TAATATTCTC
6667 TTCAAAAGT-CCTCAAACACAAGGGCA
1 TTCAAAAGTCCCT-AAACACAAGGGCA
*
6693 TTCATAAGTCCCTAAACAC-AGAGGCA
1 TTCAAAAGTCCCTAAACACAAG-GGCA
6719 TCTATACTAAAAAGT-CCTCAAACACAAGGGCA
1 --T-T-C--AAAAGTCCCT-AAACACAAGGGCA
*
6751 TTCATAAGTCCCTAAACAC-AGAGGCA
1 TTCAAAAGTCCCTAAACACAAG-GGCA
6777 TCTATACTAAAAAGT-CCTCAAACACAAGGGCA
1 --T-T-C--AAAAGTCCCT-AAACACAAGGGCA
*
6809 TTCATAAGTCCCTAAACAC-AGAGGCA
1 TTCAAAAGTCCCTAAACACAAG-GGCA
6835 TCTATACTAAAAAGT-CCTCAAACACAAGGGCA
1 --T-T-C--AAAAGTCCCT-AAACACAAGGGCA
*
6867 TTCATAAGTCCCTAAACACA
1 TTCAAAAGTCCCTAAACACA
6887 GAGTCATCTA
Statistics
Matches: 156, Mismatches: 7, Indels: 62
0.69 0.03 0.28
Matches are distributed among these distances:
25 6 0.04
26 60 0.38
27 12 0.08
28 6 0.04
29 6 0.04
30 6 0.04
31 9 0.06
32 45 0.29
33 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.19
Consensus pattern (26 bp):
TTCAAAAGTCCCTAAACACAAGGGCA
Found at i:6740 original size:58 final size:58
Alignment explanation
Indices: 6670--6898 Score: 449
Period size: 58 Copynumber: 3.9 Consensus size: 58
6660 TATTCTCTTC
6670 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
6728 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
6786 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
*
6844 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGTCATCTATA
1 AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATA
6899 TCAAAGTCCC
Statistics
Matches: 170, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
58 170 1.00
ACGTcount: A:0.41, C:0.26, G:0.14, T:0.19
Consensus pattern (58 bp):
AAAAGTCCTCAAACACAAGGGCATTCATAAGTCCCTAAACACAGAGGCATCTATACTA
Found at i:7693 original size:35 final size:35
Alignment explanation
Indices: 7650--7749 Score: 96
Period size: 35 Copynumber: 2.9 Consensus size: 35
7640 ACACATTTCA
* *
7650 TCAT-ATTCAACACTTGGG-GAGTCCAACAACCCCT
1 TCATCATTCAACACTTGGGTG-CTCCAACAACCCAT
* * *
7684 TCATCATTCAACAATTGGGTGCTCCAGCAACTCAT
1 TCATCATTCAACACTTGGGTGCTCCAACAACCCAT
* * * *
7719 TCTTCATTCAATACTTGGGCGCTTCAACAAC
1 TCATCATTCAACACTTGGGTGCTCCAACAAC
7750 AAAAATTTCA
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
34 4 0.08
35 48 0.91
36 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (35 bp):
TCATCATTCAACACTTGGGTGCTCCAACAACCCAT
Found at i:8204 original size:72 final size:73
Alignment explanation
Indices: 8096--8371 Score: 409
Period size: 72 Copynumber: 3.8 Consensus size: 73
8086 CACATGGTCC
* *
8096 TCTTCCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCTTTCGCACAATCCTTA
1 TCTTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
** *
8160 CATGATAA
66 TGTGATTA
* *
8168 TCTTCCAT-ATTGCGGTTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAACCCTTA
1 TCTTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
*
8232 TGGGATTA
66 TGTGATTA
* * *
8240 TATT-CATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTTGCAGTCCTTCACACAATCCTTA
1 TCTTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
8304 TGTGATTA
66 TGTGATTA
*
8312 TCTTCC-TCATTGCGATTGTAGCCGAGGCAGTTCCCACA-TTAGCAGTCCTTCGCACAATCC
1 TCTTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCC
8372 ATGCTACTAC
Statistics
Matches: 187, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
71 23 0.12
72 163 0.87
73 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (73 bp):
TCTTCCATCATTGCGATTGTAGCCGAGGCAGTTCCCACATTTGGCAGTCCTTCGCACAATCCTTA
TGTGATTA
Found at i:9043 original size:16 final size:16
Alignment explanation
Indices: 9022--9052 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9012 AATGGAAGGT
*
9022 TACCGCAGTAGAATGG
1 TACCGCAGCAGAATGG
9038 TACCGCAGCAGAATG
1 TACCGCAGCAGAATG
9053 TCGCCGCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (16 bp):
TACCGCAGCAGAATGG
Found at i:9115 original size:19 final size:19
Alignment explanation
Indices: 9091--9127 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9081 CAACAAAGCG
*
9091 CGAAGCAGACTATCACAAT
1 CGAAGCACACTATCACAAT
*
9110 CGAAGCTCACTATCACAA
1 CGAAGCACACTATCACAA
9128 AATGAAGGCC
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:0.30, G:0.14, T:0.16
Consensus pattern (19 bp):
CGAAGCACACTATCACAAT
Found at i:10165 original size:42 final size:40
Alignment explanation
Indices: 10111--10225 Score: 135
Period size: 39 Copynumber: 2.8 Consensus size: 40
10101 CTCTCTCCCC
* *
10111 AAAGTCCCCAAACACATATAACACAGGGGCAATTCTCCTTCT
1 AAAGT-CCCAAACACATATAACACAGGGGCAATTCT-ATACT
*
10153 AAAGTCCTCAAACACATATAACACAGAGGC-A-TCTATACT
1 AAAGTCC-CAAACACATATAACACAGGGGCAATTCTATACT
* *
10192 AAAGTCCCTAAACACATGTAACACAAGGGCAATT
1 AAAGTCCC-AAACACATATAACACAGGGGCAATT
10226 TTCTCTACAT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
38 1 0.02
39 28 0.44
40 4 0.06
41 4 0.06
42 26 0.41
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (40 bp):
AAAGTCCCAAACACATATAACACAGGGGCAATTCTATACT
Found at i:14007 original size:26 final size:27
Alignment explanation
Indices: 13946--14020 Score: 98
Period size: 26 Copynumber: 2.8 Consensus size: 27
13936 GTCATCTAGG
**
13946 GGGGCATTTTGGTCATTTTGGGCCCTA
1 GGGGCATTTTGGTCATTTTAAGCCCTA
* * *
13973 GGGGTATTTTAGTCATTTTAAG-TCTA
1 GGGGCATTTTGGTCATTTTAAGCCCTA
13999 GGGGCATTTTGGTCATTTTAAG
1 GGGGCATTTTGGTCATTTTAAG
14021 GTCCACTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 23 0.56
27 18 0.44
ACGTcount: A:0.17, C:0.12, G:0.29, T:0.41
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTTAAGCCCTA
Found at i:14212 original size:25 final size:25
Alignment explanation
Indices: 14183--14236 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
14173 AGTAGTTTGC
14183 ATTTCAGTCATGTAGCTCAAATATA
1 ATTTCAGTCATGTAGCTCAAATATA
* * * *
14208 ATTTCATTCATGTAGTTCCAATCTA
1 ATTTCAGTCATGTAGCTCAAATATA
14233 ATTT
1 ATTT
14237 AATTAACTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (25 bp):
ATTTCAGTCATGTAGCTCAAATATA
Found at i:15485 original size:29 final size:29
Alignment explanation
Indices: 15452--15512 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
15442 ATCAAAGGGC
*
15452 TTGGAGCACATGACAAGATACAAGAGGCG
1 TTGGAGCACATGACAAAATACAAGAGGCG
*
15481 TTGGAGCACATGACAAAATGCAAGAGGCG
1 TTGGAGCACATGACAAAATACAAGAGGCG
15510 TTG
1 TTG
15513 ATGACCAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.31, T:0.16
Consensus pattern (29 bp):
TTGGAGCACATGACAAAATACAAGAGGCG
Found at i:17437 original size:21 final size:21
Alignment explanation
Indices: 17411--17450 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17401 AATTCGGTGT
17411 AATTAAGTAAATTCGTAATTA
1 AATTAAGTAAATTCGTAATTA
* *
17432 AATTAAGTAATTTGGTAAT
1 AATTAAGTAAATTCGTAAT
17451 CAACTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (21 bp):
AATTAAGTAAATTCGTAATTA
Found at i:17458 original size:21 final size:21
Alignment explanation
Indices: 17411--17458 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
17401 AATTCGGTGT
*
17411 AATTAAGTAAATTCGTAATTA
1 AATTAAGTAAATTCGTAATCA
* *
17432 AATTAAGTAATTTGGTAATCA
1 AATTAAGTAAATTCGTAATCA
*
17453 ACTTAA
1 AATTAA
17459 TTCGGTGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (21 bp):
AATTAAGTAAATTCGTAATCA
Found at i:17510 original size:51 final size:51
Alignment explanation
Indices: 17432--17536 Score: 176
Period size: 51 Copynumber: 2.1 Consensus size: 51
17422 TTCGTAATTA
*
17432 AATTAAGTAATTTGGTAATCAACTTAATTCGGTGTAATTAAGTAA-ATTGGT
1 AATTAAGTAATTTGATAATCAACTTAATTCGGTGTAATTAAGTAAGA-TGGT
*
17483 AATTAAGTAATTTGATAATCAATTTAATTCGGTGTAATTAAGTAAGATGGT
1 AATTAAGTAATTTGATAATCAACTTAATTCGGTGTAATTAAGTAAGATGGT
17534 AAT
1 AAT
17537 CAACTTAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
51 50 0.98
52 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.17, T:0.39
Consensus pattern (51 bp):
AATTAAGTAATTTGATAATCAACTTAATTCGGTGTAATTAAGTAAGATGGT
Found at i:17520 original size:35 final size:35
Alignment explanation
Indices: 17481--17571 Score: 130
Period size: 35 Copynumber: 2.6 Consensus size: 35
17471 AAGTAAATTG
* * *
17481 GTAATTAAGTAATTTGATAATCAATTTAATTCGGT
1 GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
17516 GTAATTAAGTAAGA-TGGTAATCAACTTAATTCGGT
1 GTAATTAAGTAA-ATTGGTAATCAACTTAATTCGGT
*
17551 GCAATTAAGTAAATTGGTAAT
1 GTAATTAAGTAAATTGGTAAT
17572 TAAATTAAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
34 1 0.02
35 49 0.98
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (35 bp):
GTAATTAAGTAAATTGGTAATCAACTTAATTCGGT
Found at i:18198 original size:43 final size:43
Alignment explanation
Indices: 18144--18311 Score: 300
Period size: 43 Copynumber: 3.9 Consensus size: 43
18134 ATTAAATTAA
*
18144 GTAATTGGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
* *
18187 GTAATCTGGTAAACAACTTAATTCAGTGTAATTAAGTAAATTG
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
*
18230 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATGG
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
18273 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAA
1 GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAA
18312 TTCGGTGTAA
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 119 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (43 bp):
GTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAATTG
Found at i:18314 original size:18 final size:18
Alignment explanation
Indices: 18291--18326 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
18281 GTAAACAACT
18291 TAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAG
18309 TAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAG
18327 GAAATTGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (18 bp):
TAATTCGGTGTAATTAAG
Found at i:18319 original size:61 final size:61
Alignment explanation
Indices: 18248--18369 Score: 226
Period size: 61 Copynumber: 2.0 Consensus size: 61
18238 GTAAACAACT
*
18248 TAATTCGGTGTAATTAAGTAAATGGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAGGAAATGGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
*
18309 TAATTCGGTGTAATTAAGGAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
1 TAATTCGGTGTAATTAAGGAAATGGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
18370 CAAATTAGTA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (61 bp):
TAATTCGGTGTAATTAAGGAAATGGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG
Found at i:18324 original size:104 final size:104
Alignment explanation
Indices: 18205--18491 Score: 373
Period size: 104 Copynumber: 2.7 Consensus size: 104
18195 GTAAACAACT
18205 TAATTCAGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAA
1 TAATTC-GTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAA
*
18270 TGGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAG-
65 TGAGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGA
* *
18309 TAATTCGGTGTAATTAAGGAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGCAAA
1 TAATTC-GTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAA
*
18374 TTAGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGA
65 TGAGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGA
* **
18414 AAATT--TGTAATTAAGCTAAGTAATTTGGTAATTAAATTAGGTAATTAACTTAATTCGGTGTAA
1 TAATTCGTGTAATTAAG-T-A--AA-TTGGTAA-T---TT-GGTAAACAACTTAATTCGGTGTAA
*
18477 TTAAGTAAATCAGTA
56 TTAAGTAAATGAGTA
18492 GTCAACTTAA
Statistics
Matches: 161, Mismatches: 11, Indels: 14
0.87 0.06 0.08
Matches are distributed among these distances:
102 10 0.06
104 100 0.62
105 4 0.02
106 2 0.01
107 7 0.04
108 1 0.01
111 2 0.01
112 35 0.22
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.37
Consensus pattern (104 bp):
TAATTCGTGTAATTAAGTAAATTGGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGTAAAT
GAGTAATTTGGTAAACAACTTAATTCGGTGTAATTAAGA
Found at i:18357 original size:43 final size:43
Alignment explanation
Indices: 18309--18425 Score: 198
Period size: 43 Copynumber: 2.7 Consensus size: 43
18299 TGTAATTAAG
* *
18309 TAATTCGGTGTAATTAAGGAAATTGGTAATTTGGTAAACAACT
1 TAATTCGGTGTAATTAAGAAAATTAGTAATTTGGTAAACAACT
*
18352 TAATTCGGTGTAATTAAGCAAATTAGTAATTTGGTAAACAACT
1 TAATTCGGTGTAATTAAGAAAATTAGTAATTTGGTAAACAACT
*
18395 TAATTCGGTGTAATTAAGAAAATTTGTAATT
1 TAATTCGGTGTAATTAAGAAAATTAGTAATT
18426 AAGCTAAGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (43 bp):
TAATTCGGTGTAATTAAGAAAATTAGTAATTTGGTAAACAACT
Found at i:18433 original size:21 final size:21
Alignment explanation
Indices: 18409--18448 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18399 TCGGTGTAAT
18409 TAAGAAAATTT-GTAATTAAGC
1 TAAG-AAATTTGGTAATTAAGC
*
18430 TAAGTAATTTGGTAATTAA
1 TAAGAAATTTGGTAATTAA
18449 ATTAGGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.03, G:0.15, T:0.38
Consensus pattern (21 bp):
TAAGAAATTTGGTAATTAAGC
Found at i:18457 original size:21 final size:20
Alignment explanation
Indices: 18415--18459 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
18405 TAATTAAGAA
*
18415 AATTTGTAATTAAGCTAAGT
1 AATTTGTAATTAAACTAAGT
* *
18435 AATTTGGTAATTAAATTAGGT
1 AATTT-GTAATTAAACTAAGT
18456 AATT
1 AATT
18460 AACTTAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (20 bp):
AATTTGTAATTAAACTAAGT
Found at i:18478 original size:19 final size:19
Alignment explanation
Indices: 18454--18515 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
18444 ATTAAATTAG
18454 GTAATTAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
* * *
18473 GTAATTAA-GTAAATC--A
1 GTAATTAACTTAATTCGGT
* *
18489 GTAGTCAACTTAATTCGGT
1 GTAATTAACTTAATTCGGT
18508 GTAATTAA
1 GTAATTAA
18516 GTAAATCAGT
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
16 6 0.20
17 5 0.17
18 5 0.17
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (19 bp):
GTAATTAACTTAATTCGGT
Found at i:18520 original size:35 final size:35
Alignment explanation
Indices: 18454--18556 Score: 143
Period size: 35 Copynumber: 2.9 Consensus size: 35
18444 ATTAAATTAG
*
18454 GTAATTAACTTAATTCGGTGTAATTAAGTAAATCA
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATCA
*
18489 GTAGTCAACTTAATTCGGTGTAATTAAGTAAATCA
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAATCA
*** * *
18524 GTAATTGGCTTAATTTGGTGTAATTAATTAAAT
1 GTAATCAACTTAATTCGGTGTAATTAAGTAAAT
18557 AAATGACTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 60 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.39
Consensus pattern (35 bp):
GTAATCAACTTAATTCGGTGTAATTAAGTAAATCA
Found at i:23605 original size:15 final size:15
Alignment explanation
Indices: 23567--23611 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
23557 CTAACATGTT
* *
23567 TAAATAAAATATTCA
1 TAAATAAAATTTTGA
23582 TATAA-AAAATTTTGA
1 TA-AATAAAATTTTGA
23597 TAAATAAAATTTTGA
1 TAAATAAAATTTTGA
23612 CAACCACACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (15 bp):
TAAATAAAATTTTGA
Found at i:23650 original size:22 final size:22
Alignment explanation
Indices: 23625--23726 Score: 98
Period size: 22 Copynumber: 4.5 Consensus size: 22
23615 CCACACAACA
23625 AAATTTTGATAACCTCTTTATC
1 AAATTTTGATAACCTCTTTATC
* ** *
23647 AAATTTTGATAA-CTATGCCATG
1 AAATTTTGATAACCTCT-TTATC
* *
23669 AAATTTCGATAACCTCGTTATC
1 AAATTTTGATAACCTCTTTATC
* *
23691 AAATTTTGATAATTCCTCCTTATA
1 AAATTTTGATAA--CCTCTTTATC
23715 AAATTTTGATAA
1 AAATTTTGATAA
23727 ATACCATGAA
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
21 3 0.05
22 38 0.60
23 2 0.03
24 20 0.32
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (22 bp):
AAATTTTGATAACCTCTTTATC
Found at i:23734 original size:66 final size:64
Alignment explanation
Indices: 23625--23856 Score: 218
Period size: 66 Copynumber: 3.5 Consensus size: 64
23615 CCACACAACA
** * * *
23625 AAATTTTGATAACCTCTTTATCAAATTTTGATAACTATGCCATGAAATTTCGATAACCTCGTTAT
1 AAATTTTGATAACCTCACTATAAAATTTTGATAA--ATACCATGAAATTTCGATAACCTCCTTAT
*
23690 C
64 G
** *
23691 AAATTTTGATAATTCCTC-CTTATAAAATTTTGATAAATACCATGAAATTTCGATAATGTCCCTA
1 AAATTTTGATAA--CCTCAC-TATAAAATTTTGATAAATACCATGAAATTTCGATAACCTCCTTA
23755 TG
63 TG
* * * * * *
23757 AAATGTTGGTAACCACACAATTAAATTTTGATAAACACACTATGAAATTAT-GATAACCTCCTTA
1 AAATTTTGATAACCTCACTATAAAATTTTGATAAATAC-C-ATGAAATT-TCGATAACCTCCTTA
23821 TG
63 TG
*
23823 AAATTTTGATAATCC-CACTATGAAATTTTGATAA
1 AAATTTTGATAA-CCTCACTATAAAATTTTGATAA
23857 TCTCTTTATG
Statistics
Matches: 137, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
64 20 0.15
65 2 0.01
66 93 0.68
67 3 0.02
68 19 0.14
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (64 bp):
AAATTTTGATAACCTCACTATAAAATTTTGATAAATACCATGAAATTTCGATAACCTCCTTATG
Found at i:23795 original size:22 final size:22
Alignment explanation
Indices: 23715--23897 Score: 138
Period size: 22 Copynumber: 8.4 Consensus size: 22
23705 CCTCCTTATA
*
23715 AAATTTTGATAAATAC-C-ATG
1 AAATTTTGATAAACACACTATG
* *** *
23735 AAATTTCGATAATGTCCCTATG
1 AAATTTTGATAAACACACTATG
* * * * *
23757 AAATGTTGGTAACCACACAATT
1 AAATTTTGATAAACACACTATG
23779 AAATTTTGATAAACACACTATG
1 AAATTTTGATAAACACACTATG
* * *
23801 AAATTATGATAACCTC-CTTATG
1 AAATTTTGATAAACACAC-TATG
* *
23823 AAATTTTGATAATCCCACTATG
1 AAATTTTGATAAACACACTATG
* * **
23845 AAATTTTGATAATCTCTTTATG
1 AAATTTTGATAAACACACTATG
* *
23867 AAATTTTGATAAACACATTGTG
1 AAATTTTGATAAACACACTATG
23889 AAATTTTGA
1 AAATTTTGA
23898 CAACTTCCCT
Statistics
Matches: 128, Mismatches: 31, Indels: 6
0.78 0.19 0.04
Matches are distributed among these distances:
20 12 0.09
21 2 0.02
22 113 0.88
23 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTTGATAAACACACTATG
Found at i:23867 original size:66 final size:64
Alignment explanation
Indices: 23666--24067 Score: 183
Period size: 66 Copynumber: 6.3 Consensus size: 64
23656 TAACTATGCC
* * *
23666 ATGAAATTTCGATAACCTCGTTATCAAATTTTGATAATTCCTC-CTTATAAAATTTTGATAAATA
1 ATGAAATTTCGATAACCTCCTTATGAAATTTTGATAA-TCCACAC-TATAAAATTTTGAT-AAT-
23730 CC-
62 CCT
** * * * * * *
23732 ATGAAATTTCGATAATGTCCCTATGAAATGTTGGTAA-CCACACAATTAAATTTTGATAAACACA
1 ATGAAATTTCGATAACCTCCTTATGAAATTTTGATAATCCACACTATAAAATTTTGAT-AA-TC-
23796 CT
63 CT
*
23798 ATGAAATTAT-GATAACCTCCTTATGAAATTTTGATAATCC-CACTATGAAATTTTGATAATCTC
1 ATGAAATT-TCGATAACCTCCTTATGAAATTTTGATAATCCACACTATAAAATTTTGATAATC-C
23861 TTT
64 --T
* * * * * * * ** *
23864 ATGAAATTTTGATAAACACATTGTGAAATTTTGACAACTTC-C-CT-T-CGA-TTT--T--CCCT
1 ATGAAATTTCGATAACCTCCTTATGAAATTTTGATAA-TCCACACTATAAAATTTTGATAATCCT
* * * ** * *
23920 GTGAAATTTTGGT-ACCTCCCAATGAAATTTTGATAAT-TACACAATGAAAA-TTTGATAACATC
1 ATGAAATTTCGATAACCTCCTTATGAAATTTTGATAATCCACACTAT-AAAATTTTGAT-A-ATC
23982 TCT
63 -CT
* * * * * *
23985 ATGAAATTTCGATAACCTCCCTAAGAAAATTTGATAA-CCACACTATGGAAATTTTGGTACCTCT
1 ATGAAATTTCGATAACCTCCTTATGAAATTTTGATAATCCACACTAT-AAAATTTTGATA-ATC-
24049 CT
63 CT
*
24051 ATGAAATTTTGATAACC
1 ATGAAATTTCGATAACC
24068 AAACAATAAA
Statistics
Matches: 256, Mismatches: 55, Indels: 50
0.71 0.15 0.14
Matches are distributed among these distances:
54 2 0.01
55 17 0.07
56 13 0.05
58 5 0.02
59 1 0.00
60 1 0.00
61 1 0.00
63 3 0.01
64 23 0.09
65 18 0.07
66 161 0.63
67 11 0.04
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (64 bp):
ATGAAATTTCGATAACCTCCTTATGAAATTTTGATAATCCACACTATAAAATTTTGATAATCCT
Found at i:23894 original size:44 final size:44
Alignment explanation
Indices: 23625--23897 Score: 189
Period size: 44 Copynumber: 6.2 Consensus size: 44
23615 CCACACAACA
* * ** *
23625 AAATTTTGATAACCTCTTTATCAAATTTTGAT-AACTATGCCATG
1 AAATTTTGATAACCTCCTTATGAAATTTTGATAAAC-ACACTATG
* * * * * *
23669 AAATTTCGATAACCTCGTTATCAAATTTTGATAATTC-CTCCTTATA
1 AAATTTTGATAACCTCCTTATGAAATTTTGATAA-ACAC-AC-TATG
* * *** *
23715 AAATTTTGATAA-ATACC--ATGAAATTTCGATAATGTCCCTATG
1 AAATTTTGATAACCT-CCTTATGAAATTTTGATAAACACACTATG
* * * * *
23757 AAATGTTGGTAACCACAC-AATTAAATTTTGATAAACACACTATG
1 AAATTTTGATAACCTC-CTTATGAAATTTTGATAAACACACTATG
* * *
23801 AAATTATGATAACCTCCTTATGAAATTTTGATAATCCCACTATG
1 AAATTTTGATAACCTCCTTATGAAATTTTGATAAACACACTATG
* * * *
23845 AAATTTTGATAATCTCTTTATGAAATTTTGATAAACACATTGTG
1 AAATTTTGATAACCTCCTTATGAAATTTTGATAAACACACTATG
23889 AAATTTTGA
1 AAATTTTGA
23898 CAACTTCCCT
Statistics
Matches: 180, Mismatches: 39, Indels: 20
0.75 0.16 0.08
Matches are distributed among these distances:
42 14 0.08
43 5 0.03
44 143 0.79
45 3 0.02
46 15 0.08
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (44 bp):
AAATTTTGATAACCTCCTTATGAAATTTTGATAAACACACTATG
Found at i:23988 original size:22 final size:22
Alignment explanation
Indices: 23963--24066 Score: 88
Period size: 22 Copynumber: 4.7 Consensus size: 22
23953 TAATTACACA
23963 ATGAAAATTTGATAACATCTCT
1 ATGAAAATTTGATAACATCTCT
* *
23985 ATG-AAATTTCGATAACCTCCCT
1 ATGAAAATTT-GATAACATCTCT
* *
24007 AAGAAAATTTGATAACCA-CACT
1 ATGAAAATTTGATAA-CATCTCT
* * *
24029 ATGGAAATTTTGGT-ACCTCTCT
1 AT-GAAAATTTGATAACATCTCT
*
24051 ATGAAATTTTGATAAC
1 ATGAAAATTTGATAAC
24067 CAAACAATAA
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
21 17 0.26
22 32 0.49
23 16 0.25
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (22 bp):
ATGAAAATTTGATAACATCTCT
Found at i:24067 original size:44 final size:44
Alignment explanation
Indices: 23941--24152 Score: 170
Period size: 44 Copynumber: 4.8 Consensus size: 44
23931 GTACCTCCCA
* * *
23941 ATGAAATTTTGATAA-T-TACACAATGAAAATTTGATAA-CATCTCT
1 ATGAAATTTTGATAACTCT-C-CTATGAAATTTTGATAACCA-CACT
* * *
23985 ATGAAATTTCGATAAC-CTCCCTAAGAAAATTTGATAACCACACT
1 ATGAAATTTTGATAACTCT-CCTATGAAATTTTGATAACCACACT
* * * *
24029 ATGGAAATTTTGGTACCTCT-CTATGAAATTTTGATAACCAAACA
1 AT-GAAATTTTGATAACTCTCCTATGAAATTTTGATAACCACACT
* *
24073 ATAAAATTTTGATAACTAGTTCCATATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACT--CTCC-TATGAAATTTTGATAACCACACT
*
24120 A--AAATTTTGATATACT-TGCTATGAAATTTTGAT
1 ATGAAATTTTGATA-ACTCTCCTATGAAATTTTGAT
24153 GACTTCCTTA
Statistics
Matches: 139, Mismatches: 19, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
42 14 0.10
43 14 0.10
44 56 0.40
45 27 0.19
46 6 0.04
47 22 0.16
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (44 bp):
ATGAAATTTTGATAACTCTCCTATGAAATTTTGATAACCACACT
Found at i:24084 original size:66 final size:66
Alignment explanation
Indices: 23939--24088 Score: 160
Period size: 66 Copynumber: 2.3 Consensus size: 66
23929 TGGTACCTCC
* ** **
23939 CAATGAAATTTTGATAATTACACAATGAAAATTTGATAACATCTCTATGAAATTTCGATAACCTC
1 CAATAAAATTTTGATAACCACACAATGAAAATTTGATAACATCTCTATGAAATTTCGATAACCAA
*
24004 C
66 A
* * * * * *
24005 CTAAGAAAA-TTTGATAACCACACTATGGAAATTTTGGT-ACCTCTCTATGAAATTTTGATAACC
1 C-AATAAAATTTTGATAACCACACAAT-GAAAATTTGATAACATCTCTATGAAATTTCGATAACC
24068 AAA
64 AAA
24071 CAATAAAATTTTGATAAC
1 CAATAAAATTTTGATAAC
24089 TAGTTCCATA
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
65 6 0.09
66 48 0.71
67 14 0.21
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (66 bp):
CAATAAAATTTTGATAACCACACAATGAAAATTTGATAACATCTCTATGAAATTTCGATAACCAA
A
Found at i:24107 original size:47 final size:42
Alignment explanation
Indices: 24049--24152 Score: 136
Period size: 47 Copynumber: 2.4 Consensus size: 42
24039 TGGTACCTCT
*
24049 CTATGAAATTTTGATAACCAAACAATAAAATTTTGATAACTAGTTC
1 CTATGAAATTTTGATAACC--ACAATAAAATTTTGAT-A-TACTTC
* *
24095 CATATGAAATTTTGATAACCACACTAAAATTTTGATATACTTG
1 C-TATGAAATTTTGATAACCACAATAAAATTTTGATATACTTC
24138 CTATGAAATTTTGAT
1 CTATGAAATTTTGAT
24153 GACTTCCTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
42 14 0.26
43 5 0.09
44 1 0.02
45 15 0.28
46 1 0.02
47 18 0.33
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (42 bp):
CTATGAAATTTTGATAACCACAATAAAATTTTGATATACTTC
Found at i:24329 original size:22 final size:22
Alignment explanation
Indices: 24304--24358 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
24294 ACCTCCCGAA
* * *
24304 GAAATTTTGGTAACCACATTAT
1 GAAATTGTGATAACCACACTAT
24326 GAAATTGTGATAACCACACTAT
1 GAAATTGTGATAACCACACTAT
* *
24348 GATATAGTGAT
1 GAAATTGTGAT
24359 TACCTATCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (22 bp):
GAAATTGTGATAACCACACTAT
Found at i:27716 original size:33 final size:33
Alignment explanation
Indices: 27651--27717 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
27641 AACCCTAATT
* * **
27651 TTTTTTTTTAGGAAAATCGGAAAAAAGGAAAAC
1 TTTTTTTTTAGAAAAAACGGAAAAAACAAAAAC
27684 TTTTTTTTTAGAAAAAACGGAAAAAACAAAAAC
1 TTTTTTTTTAGAAAAAACGGAAAAAACAAAAAC
27717 T
1 T
27718 AATTCTTGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.49, C:0.07, G:0.13, T:0.30
Consensus pattern (33 bp):
TTTTTTTTTAGAAAAAACGGAAAAAACAAAAAC
Found at i:28019 original size:28 final size:27
Alignment explanation
Indices: 27974--28034 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
27964 TAAAGAAAAC
27974 AATTAAACTAAAAATAAAAAC-AAAGCA
1 AATTAAACTAAAAAT-AAAACTAAAGCA
** *
28001 AATTAAATCTAAATCTAAATCTAAAGCA
1 AATTAAA-CTAAAAATAAAACTAAAGCA
28029 AATTAA
1 AATTAA
28035 TAAAGCAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 11 0.38
28 18 0.62
ACGTcount: A:0.62, C:0.11, G:0.03, T:0.23
Consensus pattern (27 bp):
AATTAAACTAAAAATAAAACTAAAGCA
Found at i:30355 original size:156 final size:154
Alignment explanation
Indices: 30170--30567 Score: 444
Period size: 156 Copynumber: 2.6 Consensus size: 154
30160 TGGCTTGGTT
* * * * *
30170 CGAGCCCTCCTTCATGGTGAACTAGGTTTCACACCCCAAACTGTCCTTAAATGAAAAACATGCAG
1 CGAGCTCTCCTTCATGGTGAACTTGGTTTCTCTCCCCAAACTGTCCTTAAATGAAAAACATGCAT
* *** ** *
30235 AAGTTTTTCAT-TCTAAGTTTGATTGAGATGAAACTTTTCCA-AG-GGCCTTAGATTATTTCCAC
66 AAGTTTTTAATCT-TAAGTCCAATAAAGATG-AA--TTTCCACAGAGG-CTTAGATTATCTCCAC
*
30297 AAGACTATGGAAAAAATTCTAACTAAAAC
126 AAAACTATGGAAAAAATTCTAACTAAAAC
* * * *
30326 CGAGCTCTCCTTGATGGTGAACTTGGTTTCTCTCTCCAAACTGTCCTTAAAAGAAAAACTTGCAT
1 CGAGCTCTCCTTCATGGTGAACTTGGTTTCTCTCCCCAAACTGTCCTTAAATGAAAAACATGCAT
* * *
30391 AAGTTTATAATCTTAAGTCCAATAAAGGTGAATTTCCAGCAGTAGGCTTAGATTATCTCCATAAA
66 AAGTTTTTAATCTTAAGTCCAATAAAGATGAATTTCCA-CAG-AGGCTTAGATTATCTCCACAAA
*
30456 ACTATGGAAAAAATTCTAAGTAAAAC
129 ACTATGGAAAAAATTCTAACTAAAAC
* * * *
30482 CGAACTC-CCTTTCATAGTGAAGTTGGTTTCTCTCCCCGAACTGTCCTTAAATGAAAAACATGCA
1 CGAGCTCTCC-TTCATGGTGAACTTGGTTTCTCTCCCCAAACTGTCCTTAAATGAAAAACATGCA
* *
30546 TATGTTTTTTTATCTTAAGTCC
65 TAAG-TTTTTAATCTTAAGTCC
30568 GTTTGACATG
Statistics
Matches: 203, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
153 6 0.03
155 6 0.03
156 173 0.85
157 18 0.09
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.32
Consensus pattern (154 bp):
CGAGCTCTCCTTCATGGTGAACTTGGTTTCTCTCCCCAAACTGTCCTTAAATGAAAAACATGCAT
AAGTTTTTAATCTTAAGTCCAATAAAGATGAATTTCCACAGAGGCTTAGATTATCTCCACAAAAC
TATGGAAAAAATTCTAACTAAAAC
Found at i:36172 original size:20 final size:20
Alignment explanation
Indices: 36123--36173 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
36113 ACCGTTTAAG
*
36123 GGATTAACCCGTTGAAAACT
1 GGATTAACCCGTTGAAAACC
*
36143 GG-TGTGACCCGTT-AAAATCC
1 GGAT-TAACCCGTTGAAAA-CC
36163 GGATTAACCCG
1 GGATTAACCCG
36174 GTGACCCGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 5 0.20
20 19 0.76
21 1 0.04
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
GGATTAACCCGTTGAAAACC
Found at i:41583 original size:6 final size:6
Alignment explanation
Indices: 41572--41603 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
41562 ATTAATTTGC
41572 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
41604 GCTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:41933 original size:22 final size:23
Alignment explanation
Indices: 41890--41934 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41880 GCGCAAAAAC
* *
41890 CAAGCTCCGTGCTTATTTTCTCT
1 CAAGCTCCGCGCCTATTTTCTCT
41913 CAAGCTCCGCGCCT-TTTTCTCT
1 CAAGCTCCGCGCCTATTTTCTCT
41935 TTTTCATCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.11, C:0.36, G:0.13, T:0.40
Consensus pattern (23 bp):
CAAGCTCCGCGCCTATTTTCTCT
Found at i:43020 original size:30 final size:30
Alignment explanation
Indices: 42984--43040 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
42974 ATCCATTGGC
42984 CGGTTGTGGCCGGTTACCCCATGCGATGGT
1 CGGTTGTGGCCGGTTACCCCATGCGATGGT
* *
43014 CGGTTGTGGCCGGTTGCTCCATGCGAT
1 CGGTTGTGGCCGGTTACCCCATGCGAT
43041 AGCCCTTGCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.09, C:0.26, G:0.37, T:0.28
Consensus pattern (30 bp):
CGGTTGTGGCCGGTTACCCCATGCGATGGT
Found at i:54191 original size:22 final size:22
Alignment explanation
Indices: 54070--54478 Score: 156
Period size: 22 Copynumber: 18.7 Consensus size: 22
54060 AACCTTATTC
* * * *
54070 AATTTTGTTAACCTCCCTAAGG
1 AATTTTGATAACCTCCATATGA
*
54092 AATTTTGA-ATACCTCAATATGA
1 AATTTTGATA-ACCTCCATATGA
*
54114 AATTTTGATAACTTCC-TAATGA
1 AATTTTGATAACCTCCAT-ATGA
**
54136 AATTTTGATAACCAACACTATGA
1 AATTTTGATAACCTCCA-TATGA
*
54159 GATGTTT-ATAACCTCCATATGA
1 AAT-TTTGATAACCTCCATATGA
* * * **
54181 TATATTGATAACCACGTTATG-
1 AATTTTGATAACCTCCATATGA
* * *
54202 AATATTTAAAAACCTACATATG-
1 AAT-TTTGATAACCTCCATATGA
* * *
54224 AATTGTT-ACTAA-TTACACTCTGA
1 AATT-TTGA-TAACCTCCA-TATGA
54247 AATTTTGATAA--TCACACTATGA
1 AATTTTGATAACCTC-CA-TATGA
*
54269 AATTGTGATAACCTCGC-TATGA
1 AATTTTGATAACCTC-CATATGA
* * *
54291 AATTTTGATAAATCTTTC-TATAA
1 AATTTTGAT-AA-CCTCCATATGA
* *
54314 AATTTTGATAAACCTCCCTATAA
1 AATTTTGAT-AACCTCCATATGA
* * * *
54337 AATTTTGTTAACTTTCTTATGA
1 AATTTTGATAACCTCCATATGA
* *
54359 AATCTTGATAA----C-TA-CA
1 AATTTTGATAACCTCCATATGA
*
54375 AATTTTGATAACCTCCCTATGA
1 AATTTTGATAACCTCCATATGA
**
54397 TTTTTTGATAACCT-CATTATGA
1 AATTTTGATAACCTCCA-TATGA
* * *
54419 AATTTTGTTAATCTCCCTATGA
1 AATTTTGATAACCTCCATATGA
* * *
54441 TATTTTGATCTACAT--AGTATGA
1 AATTTTGAT-AACCTCCA-TATGA
54463 AATTTTGATAACCTCC
1 AATTTTGATAACCTCC
54479 CCAGAAATAC
Statistics
Matches: 290, Mismatches: 66, Indels: 61
0.70 0.16 0.15
Matches are distributed among these distances:
16 11 0.04
17 2 0.01
18 1 0.00
20 1 0.00
21 19 0.07
22 192 0.66
23 55 0.19
24 9 0.03
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (22 bp):
AATTTTGATAACCTCCATATGA
Found at i:54292 original size:44 final size:44
Alignment explanation
Indices: 54244--54685 Score: 208
Period size: 44 Copynumber: 10.4 Consensus size: 44
54234 AATTACACTC
* *
54244 TGAAATTTTGATAATCACACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAATCTCACTATGAAATTTTGATAACCTCGCTA
** * *
54288 TGAAATTTTGATAAATCTTTCTATAAAATTTTGATAAACCTCCCTA
1 TGAAATTTTGAT-AATCTCACTATGAAATTTTGAT-AACCTCGCTA
* * * * *
54334 TAAAATTTTGTTAACTTTC-TTATGAAATCTTGATAA-----CTA
1 TGAAATTTTGATAA-TCTCACTATGAAATTTTGATAACCTCGCTA
* * * ** **
54373 -CAAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTA
1 TGAAATTTTGATAATCTCACTATGAAATTTTGATAACCTCGCTA
* * * * * *
54416 TGAAATTTTGTTAATCTCCCTATGATATTTTGATCTACATAG-TA
1 TGAAATTTTGATAATCTCACTATGAAATTTTGAT-AACCTCGCTA
* * * *
54460 TGAAATTTTGATAACCTCCCCA-G-AA-----AT-A-C-CACTA
1 TGAAATTTTGATAATCTCACTATGAAATTTTGATAACCTCGCTA
* * * * **
54494 TGAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTA
1 TGAAA-TTTTGATAATCTCACTATGAAATTTTGATAACCTCGCTA
* ** * * * * *
54538 TGAAATTTTGATAACCTCTTTATAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAATCTCACTATGAAATTTTGATAACCTCGCTA
* * * * * *
54582 TGAAATTCTGATAATCACATTAAGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAATCTCACTATGAAATTTTGATAACCTCGCTA
* * *
54626 TGAAATTTTGATAA-CAACACTATGAAACTTTGATAATCTTC-CTA
1 TGAAATTTTGATAATC-TCACTATGAAATTTTGATAA-CCTCGCTA
54670 T-AAATTTTGATAATCT
1 TGAAATTTTGATAATCT
54686 GATCTCTATG
Statistics
Matches: 296, Mismatches: 75, Indels: 55
0.69 0.18 0.13
Matches are distributed among these distances:
34 12 0.04
35 7 0.02
36 2 0.01
37 4 0.01
38 24 0.08
39 3 0.01
41 2 0.01
42 2 0.01
43 22 0.07
44 160 0.54
45 37 0.12
46 21 0.07
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.40
Consensus pattern (44 bp):
TGAAATTTTGATAATCTCACTATGAAATTTTGATAACCTCGCTA
Found at i:54316 original size:23 final size:22
Alignment explanation
Indices: 54285--54369 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
54275 GATAACCTCG
*
54285 CTATGAAATTTTGATAAATCTTT
1 CTATAAAATTTTGATAAA-CTTT
**
54308 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAA-CTTT
*
54331 CTATAAAATTTTG-TTAACTTT
1 CTATAAAATTTTGATAAACTTT
* *
54352 CTTATGAAATCTTGATAA
1 C-TATAAAATTTTGATAA
54370 CTACAAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 3 0.06
22 13 0.26
23 34 0.68
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACTTT
Found at i:54368 original size:45 final size:45
Alignment explanation
Indices: 54246--54369 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
54236 TTACACTCTG
*** * *
54246 AAATTTTGAT-AATCACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTTCTATGAAATT-TGATAAACCTCCCTATA
*
54290 AAATTTTGATAAATCTTTCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTTCTATGAAA-TTTGATAAACCTCCCTATA
*
54336 AAATTTTG-TTAA-CTTTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTTC-TATGAAAT-TTGATAA
54370 CTACAAATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
44 16 0.24
45 31 0.46
46 20 0.30
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAAATCTTTCTATGAAATTTGATAAACCTCCCTATA
Found at i:54651 original size:22 final size:22
Alignment explanation
Indices: 54489--54728 Score: 112
Period size: 22 Copynumber: 10.9 Consensus size: 22
54479 CCAGAAATAC
54489 CACTATGAAATTTTTG-TAATCA
1 CACTATGAAA-TTTTGATAATCA
* * * * *
54511 CATTTTGAAAATTTGATAACCT
1 CACTATGAAATTTTGATAATCA
** * *
54533 CTTTATGAAATTTTGATAACCT
1 CACTATGAAATTTTGATAATCA
** * * * * *
54555 CTTTATAAAATTTTGTTGACCC
1 CACTATGAAATTTTGATAATCA
* *
54577 CTCTATGAAATTCTGATAATCA
1 CACTATGAAATTTTGATAATCA
* * * * *
54599 CATTAAGTAATTTTGATAACCT
1 CACTATGAAATTTTGATAATCA
* *
54621 CGCTTTGAAATTTTGATAA-CAA
1 CACTATGAAATTTTGATAATC-A
* *
54643 CACTATGAAACTTTGATAATCTT
1 CACTATGAAATTTTGATAATC-A
54666 C-CTAT-AAATTTTGATAATCTGA
1 CACTATGAAATTTTGATAATC--A
* *
54688 TCTCTATGAAATTTCGATAATCA
1 -CACTATGAAATTTTGATAATCA
* *
54711 CTCTATGAGA-TTTGATAA
1 CACTATGAAATTTTGATAA
54729 CCTTTTATCA
Statistics
Matches: 168, Mismatches: 43, Indels: 15
0.74 0.19 0.07
Matches are distributed among these distances:
21 25 0.15
22 122 0.73
23 4 0.02
24 4 0.02
25 13 0.08
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (22 bp):
CACTATGAAATTTTGATAATCA
Found at i:54820 original size:22 final size:21
Alignment explanation
Indices: 54795--54844 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
54785 CAACACTATA
* *
54795 AAATTTCGATAACCTCCCCATG
1 AAATTTAG-TAACCTCCCAATG
*
54817 AAATATTAGTAACCTCCTAATG
1 AAAT-TTAGTAACCTCCCAATG
54839 AAATTT
1 AAATTT
54845 TGTTAACCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 19 0.79
23 3 0.12
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (21 bp):
AAATTTAGTAACCTCCCAATG
Found at i:54851 original size:22 final size:20
Alignment explanation
Indices: 54790--54865 Score: 53
Period size: 22 Copynumber: 3.5 Consensus size: 20
54780 CATAACAACA
* *
54790 CTATAAAATTTCGATAACCTCC
1 CTATGAAATTTAG-TAACCT-C
*
54812 CCATGAAATATTAGTAACCTC
1 CTATGAAAT-TTAGTAACCTC
* *
54833 CTAATGAAATTTTGTTAACCAC
1 CT-ATGAAATTTAG-TAACCTC
54855 ACTATGAAATT
1 -CTATGAAATT
54866 CTTATAACCT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 5 0.11
22 34 0.77
23 5 0.11
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (20 bp):
CTATGAAATTTAGTAACCTC
Found at i:54991 original size:24 final size:22
Alignment explanation
Indices: 54937--55039 Score: 75
Period size: 22 Copynumber: 4.6 Consensus size: 22
54927 AATTAACCAC
*
54937 CCTATGAAATTTCAATAATCAA
1 CCTATGAAATTTTAATAATCAA
* * *
54959 CCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTAATAA--TCAA
**
54983 CCTATGAAATTTTGGTAA-CAA
1 CCTATGAAATTTTAATAATCAA
* **
55004 CACTATGAAATTTTGATAA-CTT
1 C-CTATGAAATTTTAATAATCAA
55026 CCATATGAAATTTT
1 CC-TATGAAATTTT
55040 GGTAACCACA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
21 3 0.05
22 45 0.69
24 17 0.26
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (22 bp):
CCTATGAAATTTTAATAATCAA
Found at i:55012 original size:22 final size:22
Alignment explanation
Indices: 54984--55111 Score: 100
Period size: 22 Copynumber: 5.8 Consensus size: 22
54974 TAACCTGATC
*
54984 CTATGAAATTTTGGTAACAACA
1 CTATGAAATTTTGATAACAACA
**
55006 CTATGAAATTTTGATAACTTC-
1 CTATGAAATTTTGATAACAACA
* *
55027 CATATGAAATTTTGGTAACCACA
1 C-TATGAAATTTTGATAACAACA
* **
55050 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACAACA
* * * *
55071 CTCATGAAATTATAATAACTA-T
1 CT-ATGAAATTTTGATAACAACA
55093 CTCATGAAATTTTGATAAC
1 CT-ATGAAATTTTGATAAC
55112 CACATAGAGA
Statistics
Matches: 86, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
21 3 0.03
22 82 0.95
23 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACAACA
Found at i:55014 original size:46 final size:44
Alignment explanation
Indices: 54937--55112 Score: 162
Period size: 44 Copynumber: 4.0 Consensus size: 44
54927 AATTAACCAC
*** * *
54937 CCTATGAAATTTCAATAATCAAC-CTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAA-CAACACTATGAAATTTTGATAACCT--T
54983 CCTATGAAATTTTGGTAACAACACTATGAAATTTTGATAA-CTT
1 CCTATGAAATTTTGGTAACAACACTATGAAATTTTGATAACCTT
* *
55026 CCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-T
1 CC-TATGAAATTTTGGTAACAACACTATGAAATTTTGATAACCTT
* ** * *
55070 CCTCATGAAATTATAATAACTA-TCTCATGAAATTTTGATAACC
1 CCT-ATGAAATTTTGGTAACAACACT-ATGAAATTTTGATAACC
55113 ACATAGAGAC
Statistics
Matches: 112, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
43 6 0.05
44 69 0.62
45 7 0.06
46 30 0.27
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.35
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACAACACTATGAAATTTTGATAACCTT
Found at i:55715 original size:37 final size:38
Alignment explanation
Indices: 55642--55717 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
55632 AACCGGAGAC
* *
55642 AGACAAAAAGCAAAATTACATACAACGATTGGAAACAA
1 AGACAAAAAGCAAAATTAAATACAACGATTGAAAACAA
* **
55680 AGACAAAAGGCAAAATTAAATAGGACG-TTGAAAACAA
1 AGACAAAAAGCAAAATTAAATACAACGATTGAAAACAA
55717 A
1 A
55718 AAGTTAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
37 10 0.30
38 23 0.70
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (38 bp):
AGACAAAAAGCAAAATTAAATACAACGATTGAAAACAA
Found at i:55876 original size:31 final size:31
Alignment explanation
Indices: 55841--55899 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
55831 GGCAATTTAG
55841 AAATATGTTTTAGAAAA-AAGGGTACAATTGA
1 AAATATGTTTTA-AAAATAAGGGTACAATTGA
55872 AAATATGTTTTAAAAATAAGGGTACAAT
1 AAATATGTTTTAAAAATAAGGGTACAAT
55900 CGGAAAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (31 bp):
AAATATGTTTTAAAAATAAGGGTACAATTGA
Found at i:59468 original size:19 final size:19
Alignment explanation
Indices: 59432--59466 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59422 AAAACCTTTC
59432 TTCTCTCTTTTTGTTTTTG
1 TTCTCTCTTTTTGTTTTTG
59451 TTCTCT-TTTTT-TTTTT
1 TTCTCTCTTTTTGTTTTT
59467 TTTTTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (19 bp):
TTCTCTCTTTTTGTTTTTG
Found at i:62458 original size:36 final size:35
Alignment explanation
Indices: 62411--62529 Score: 133
Period size: 36 Copynumber: 3.4 Consensus size: 35
62401 TCTTTTCTAG
*
62411 ATTAAGCTCTTTATTGACTTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATTGACTTCACTTAATTACC-TGA
62447 ATTAAGTTCTTTATT--C-T-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTTCACTTAATTA-CCTGA
*
62479 ATTAAG-CCTTTTATTGA-TCTCACTTAATTACACTGA
1 ATTAAGTTC-TTTATTGACT-TCACTTAATTAC-CTGA
62515 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
62530 CTACTTAATT
Statistics
Matches: 71, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
31 1 0.01
32 24 0.34
33 3 0.04
34 1 0.01
35 2 0.03
36 39 0.55
37 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.46
Consensus pattern (35 bp):
ATTAAGTTCTTTATTGACTTCACTTAATTACCTGA
Found at i:62473 original size:32 final size:32
Alignment explanation
Indices: 62432--62544 Score: 131
Period size: 32 Copynumber: 3.4 Consensus size: 32
62422 TATTGACTTC
62432 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
1 ACTTAATTACCTTGAATTAAGTTCTTTATTCT
* *
62464 ACTTAATTACCCTGAATTAAG-CCTTTTATTGATCT
1 ACTTAATTACCTTGAATTAAGTTC-TTTA-T--TCT
62499 CACTTAATTACAC-TGAATTAAGTTCTTTATTCT
1 -ACTTAATTAC-CTTGAATTAAGTTCTTTATTCT
*
62532 ACTTAATTTCCTT
1 ACTTAATTACCTT
62545 TCCTAAAATT
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
31 2 0.03
32 34 0.49
33 4 0.06
35 4 0.06
36 23 0.33
37 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (32 bp):
ACTTAATTACCTTGAATTAAGTTCTTTATTCT
Found at i:62492 original size:68 final size:68
Alignment explanation
Indices: 62411--62539 Score: 210
Period size: 68 Copynumber: 1.9 Consensus size: 68
62401 TCTTTTCTAG
62411 ATTAAGCTCTTTATTGA-CTTCACTTAATTAC-CTTGAATTAAGTTCTTTATTCTACTTAATTAC
1 ATTAAGCTCTTTATTGATC-TCACTTAATTACAC-TGAATTAAGTTCTTTATTCTACTTAATTAC
62474 CCTGA
64 CCTGA
62479 ATTAAGC-CTTTTATTGATCTCACTTAATTACACTGAATTAAGTTCTTTATTCTACTTAATT
1 ATTAAGCTC-TTTATTGATCTCACTTAATTACACTGAATTAAGTTCTTTATTCTACTTAATT
62540 TCCTTTCCTA
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
67 1 0.02
68 55 0.95
69 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (68 bp):
ATTAAGCTCTTTATTGATCTCACTTAATTACACTGAATTAAGTTCTTTATTCTACTTAATTACCC
TGA
Found at i:62615 original size:36 final size:36
Alignment explanation
Indices: 62568--63174 Score: 847
Period size: 36 Copynumber: 16.9 Consensus size: 36
62558 CATGTGTCTT
* * *
62568 TTTACTTAATTTCCTTGAAATTAAGTCAGTCTTTCC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
62604 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* * *
62640 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* *
62676 TTTACTTAATTTCCTTGAAATCAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
*
62712 TTTA-CTCAATTTCCTTGAAATCAAGCCAGTCTTTTC
1 TTTACCT-AATTTCCTTGAAATTAAGCCAGTCTTTTC
* *
62748 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* * *
62784 TTTACCTAGTTTCCTTGAAACTAAGCCAATCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* **
62820 TTTACTTAATTTCCTTGAAATTAAATCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* *
62856 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
*
62892 TTTACTTAATTTCCTTGAAATTAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* *
62928 TTTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* * *
62964 TTTACTTAATTTCCTTGAAATTAAACCAGTCTATTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* * *
63000 TTTACCTAGTTTCCCTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* * *
63036 TGTACCTAGTTTCCTTGAAACTAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* *
63072 TTTACTTAATTTCCTTGAAATCAAGCCAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* * * *
63108 TATACTTAATTTCCTTTAAATTAAGACAGTCTTTTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
* *
63144 TTTACCTAGTTTCCTTGAAACTAAGCCAGTC
1 TTTACCTAATTTCCTTGAAATTAAGCCAGTC
63175 CTCTAATGTT
Statistics
Matches: 508, Mismatches: 61, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
35 1 0.00
36 505 0.99
37 2 0.00
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (36 bp):
TTTACCTAATTTCCTTGAAATTAAGCCAGTCTTTTC
Found at i:66459 original size:22 final size:22
Alignment explanation
Indices: 66414--66460 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
66404 AAAAAGAAAG
* *
66414 TTGCGTCGATAAAAAAATGTTT
1 TTGCGTCAATAAAAAAAAGTTT
66436 TTGCGTCAATAAAAAAAAAGTTT
1 TTGCGTCAAT-AAAAAAAAGTTT
66459 TT
1 TT
66461 TCCGTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (22 bp):
TTGCGTCAATAAAAAAAAGTTT
Found at i:69979 original size:10 final size:10
Alignment explanation
Indices: 69964--70006 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
69954 TCGACACCAA
69964 GCCATGCCCG
1 GCCATGCCCG
69974 GCCATGTCCGCG
1 GCCATG-CC-CG
*
69986 CACCATGCCCG
1 -GCCATGCCCG
69997 GCCATGCCCG
1 GCCATGCCCG
70007 ACCAATGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 15 0.54
11 4 0.14
12 4 0.14
13 5 0.18
ACGTcount: A:0.12, C:0.49, G:0.28, T:0.12
Consensus pattern (10 bp):
GCCATGCCCG
Found at i:72260 original size:10 final size:10
Alignment explanation
Indices: 72245--72270 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
72235 AGTCGCTGCC
72245 AAATTCCAGA
1 AAATTCCAGA
72255 AAATTCCAGA
1 AAATTCCAGA
72265 AAATTC
1 AAATTC
72271 TAGAGTCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (10 bp):
AAATTCCAGA
Found at i:73221 original size:6 final size:6
Alignment explanation
Indices: 73210--73239 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
73200 ATTCTGCTTC
73210 AGATTT AGATTT AGATTT AGATTT AGATTT
1 AGATTT AGATTT AGATTT AGATTT AGATTT
73240 GCTTTGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
AGATTT
Found at i:74032 original size:27 final size:27
Alignment explanation
Indices: 73979--74032 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
73969 ATTGTTTTTC
**
73979 TTGTATTGTCTGTTTTCCTTTGTCTTG
1 TTGTATTGTCTGTGCTCCTTTGTCTTG
*
74006 TTGTATTGCTCTGTGCTCTTTTG-CTTG
1 TTGTATTG-TCTGTGCTCCTTTGTCTTG
74033 CCGCCTGCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.04, C:0.17, G:0.20, T:0.59
Consensus pattern (27 bp):
TTGTATTGTCTGTGCTCCTTTGTCTTG
Found at i:76105 original size:64 final size:64
Alignment explanation
Indices: 76001--76124 Score: 239
Period size: 64 Copynumber: 1.9 Consensus size: 64
75991 CTGTTAAGAG
76001 AAAAGAGTTACATTAGGCAATTACATAGGGGCATTCCATGCATATTCAAGCCAAAGACATAGAT
1 AAAAGAGTTACATTAGGCAATTACATAGGGGCATTCCATGCATATTCAAGCCAAAGACATAGAT
*
76065 AAAAGAGTTACATTAGGCAATTACATAGGGGCATTTCATGCATATTCAAGCCAAAGACAT
1 AAAAGAGTTACATTAGGCAATTACATAGGGGCATTCCATGCATATTCAAGCCAAAGACAT
76125 TCGCATGTCA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (64 bp):
AAAAGAGTTACATTAGGCAATTACATAGGGGCATTCCATGCATATTCAAGCCAAAGACATAGAT
Found at i:79889 original size:53 final size:53
Alignment explanation
Indices: 79822--80083 Score: 472
Period size: 53 Copynumber: 4.9 Consensus size: 53
79812 GTAATCAGTA
79822 ATCAGTAAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
1 ATCAGT-AAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
* *
79876 ATTAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAAAG-C
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
*
79928 TATCAGTAAAAAGAGTAAGAAACAGTATTCAGTAAAAAGAGTAAGAAAAGAGTC
1 -ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
79982 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
80035 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
1 ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAG
80084 CGCAATAGTA
Statistics
Matches: 200, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
52 1 0.00
53 193 0.96
54 6 0.03
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (53 bp):
ATCAGTAAAAAGAGTAAGAAACAATATTCAGTAAAAAGAGTAAGAAAAGAGTC
Found at i:80093 original size:26 final size:26
Alignment explanation
Indices: 79821--80093 Score: 185
Period size: 26 Copynumber: 10.3 Consensus size: 26
79811 AGTAATCAGT
*
79821 AATCAGTAAAAAAGAGTAAG-AAAC-A
1 AATCAGT-AAAAAGAGTAAGAAAACGC
*
79846 ATATTCAGTAAAAAGAGTAAGAAAAGAGTC
1 A-A-TCAGTAAAAAGAGTAAGAAAA-CG-C
* *
79876 -ATTAGTAAAAAGAGTAAG-AAAC-A
1 AATCAGTAAAAAGAGTAAGAAAACGC
*
79899 ATATTCAGTAAAAAGAGTAAGAAAAAAGC
1 A-A-TCAGTAAAAAGAGTAAG-AAAACGC
* *
79928 TATCAGTAAAAAGAGTAAG-AAACAGT
1 AATCAGTAAAAAGAGTAAGAAAAC-GC
* *
79954 ATTCAGTAAAAAGAGTAAGAAAAGAGTC
1 AATCAGTAAAAAGAGTAAGAAAA-CG-C
*
79982 -ATCAGTAAAAAGAGTAAG-AAAC-A
1 AATCAGTAAAAAGAGTAAGAAAACGC
*
80005 ATATTCAGTAAAAAGAGTAAGAAAAGAGTC
1 A-A-TCAGTAAAAAGAGTAAGAAAA-CG-C
*
80035 -ATCAGTAAAAAGAGTAAG-AAAC-A
1 AATCAGTAAAAAGAGTAAGAAAACGC
80058 ATATTCAGTAAAAAGAGTAAGAAAAGCGC
1 A-A-TCAGTAAAAAGAGTAAGAAAA-CGC
80087 AAT-AGTA
1 AATCAGTA
80094 GTCAACAAAG
Statistics
Matches: 196, Mismatches: 23, Indels: 57
0.71 0.08 0.21
Matches are distributed among these distances:
25 7 0.04
26 94 0.48
27 86 0.44
28 8 0.04
29 1 0.01
ACGTcount: A:0.57, C:0.07, G:0.19, T:0.17
Consensus pattern (26 bp):
AATCAGTAAAAAGAGTAAGAAAACGC
Found at i:80172 original size:7 final size:7
Alignment explanation
Indices: 80162--80392 Score: 84
Period size: 7 Copynumber: 32.9 Consensus size: 7
80152 AAAGGCAATC
80162 AGTAAAG
1 AGTAAAG
80169 AGTAAA-
1 AGTAAAG
*
80175 ATGGTAAAA
1 A--GTAAAG
*
80184 AGTAATG
1 AGTAAAG
**
80191 -GTAATC
1 AGTAAAG
*
80197 AGTAAAC
1 AGTAAAG
*
80204 AGTAAAAT
1 AGT-AAAG
80212 AGTAAAG
1 AGTAAAG
*
80219 AGTAAAA
1 AGTAAAG
**
80226 AGTAATC
1 AGTAAAG
80233 AGTAAAG
1 AGTAAAG
80240 AG-AAATG
1 AGTAAA-G
80247 -GTAAAG
1 AGTAAAG
80253 AGTAATAG
1 AGTAA-AG
*
80261 AG-AAATT
1 AGTAAA-G
80268 AGTAAAG
1 AGTAAAG
*
80275 A-AAAATG
1 AGTAAA-G
80282 -GTAAAG
1 AGTAAAG
80288 AGTAAAG
1 AGTAAAG
**
80295 AGTAATT
1 AGTAAAG
80302 AGTAAAG
1 AGTAAAG
* *
80309 -GAAAAT
1 AGTAAAG
*
80315 AGTAAGG
1 AGTAAAG
*
80322 AGTGAAG
1 AGTAAAG
**
80329 AGTAATT
1 AGTAAAG
*
80336 AGTAAAA
1 AGTAAAG
80343 ATGGTAAAG
1 A--GTAAAG
80352 -GATAAAG
1 AG-TAAAG
**
80359 AGTAATC
1 AGTAAAG
80366 AGTAAAG
1 AGTAAAG
**
80373 AAAAAAG
1 AGTAAAG
*
80380 GGTAAAG
1 AGTAAAG
80387 AGTAAA
1 AGTAAA
80393 ATATTAATCA
Statistics
Matches: 163, Mismatches: 42, Indels: 38
0.67 0.17 0.16
Matches are distributed among these distances:
6 21 0.13
7 117 0.72
8 19 0.12
9 6 0.04
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (7 bp):
AGTAAAG
Found at i:80199 original size:35 final size:35
Alignment explanation
Indices: 80158--80407 Score: 241
Period size: 35 Copynumber: 7.3 Consensus size: 35
80148 TTGAAAAGGC
* *
80158 AATCAGTAAAGAGTAAAATGGTAAAAAGTAATG-GT
1 AATCAGTAAAGAG-AAAATGGTAAAGAGTAAAGAGT
* * *
80193 AATCAGTAAACAGTAAAATAGTAAAGAGTAAAAAGT
1 AATCAGTAAAGAG-AAAATGGTAAAGAGTAAAGAGT
*
80229 AATCAGTAAAGAG-AAATGGTAAAGAGTAATAGAGA
1 AATCAGTAAAGAGAAAATGGTAAAGAGTAA-AGAGT
*
80264 AATTAGTAAAGA-AAAATGGTAAAGAGTAAAGAGT
1 AATCAGTAAAGAGAAAATGGTAAAGAGTAAAGAGT
* * * *
80298 AATTAGTAAAG-GAAAATAGTAAGGAGTGAAGAGT
1 AATCAGTAAAGAGAAAATGGTAAAGAGTAAAGAGT
*
80332 AATTAGT----A-AAAATGGTAAAG-GATAAAGAGT
1 AATCAGTAAAGAGAAAATGGTAAAGAG-TAAAGAGT
* * * *
80362 AATCAGTAAAGAAAAAAGGGTAAAGAGTAAAATATT
1 AATCAGTAAAGAGAAAATGGTAAAGAGT-AAAGAGT
80398 AATCAGTAAA
1 AATCAGTAAA
80408 AAGTAATGGC
Statistics
Matches: 181, Mismatches: 21, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
29 1 0.01
30 23 0.13
34 57 0.31
35 70 0.39
36 30 0.17
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.20
Consensus pattern (35 bp):
AATCAGTAAAGAGAAAATGGTAAAGAGTAAAGAGT
Found at i:80217 original size:15 final size:14
Alignment explanation
Indices: 80197--80238 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
80187 AATGGTAATC
80197 AGTAAACAGTAAAA
1 AGTAAACAGTAAAA
*
80211 TAGTAAAGAGTAAAA
1 -AGTAAACAGTAAAA
*
80226 AGTAATCAGTAAA
1 AGTAAACAGTAAA
80239 GAGAAATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.19
Consensus pattern (14 bp):
AGTAAACAGTAAAA
Found at i:81364 original size:17 final size:19
Alignment explanation
Indices: 81342--81384 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
81332 TGGCCATCTC
81342 AAGAAAGAC-T-GTCCGAA
1 AAGAAAGACTTGGTCCGAA
* *
81359 AAGAAAGGCTTGGTTCGAA
1 AAGAAAGACTTGGTCCGAA
81378 AAGAAAG
1 AAGAAAG
81385 GTACATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 1 0.05
19 13 0.59
ACGTcount: A:0.47, C:0.12, G:0.28, T:0.14
Consensus pattern (19 bp):
AAGAAAGACTTGGTCCGAA
Done.