Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006848.1 Hibiscus syriacus cultivar Beakdansim tig00017415_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: 62605
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2546 original size:23 final size:23
Alignment explanation
Indices: 2514--2577 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
2504 CAGCTCATAT
2514 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
2537 AATTGTACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
2560 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
2578 TATAATAATG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:6011 original size:16 final size:16
Alignment explanation
Indices: 5992--6037 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
5982 AAAAAACAAT
*
5992 TAATAATTCTAATAAA
1 TAATAATTATAATAAA
6008 TAATAATTAT-ATAAA
1 TAATAATTATAATAAA
* *
6023 T-ATTATTTTAATAAA
1 TAATAATTATAATAAA
6038 AAAATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 6 0.23
15 11 0.42
16 9 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATTATAATAAA
Found at i:6055 original size:15 final size:14
Alignment explanation
Indices: 6036--6087 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
6026 TATTTTAATA
6036 AAAAAATAATATTT
1 AAAAAATAATATTT
*
6050 ACAAAAT-ATATTAAT
1 AAAAAATAATATT--T
*
6065 ATAAAATAACTATTT
1 AAAAAATAA-TATTT
6080 AAAAAATA
1 AAAAAATA
6088 CTAACATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
13 5 0.16
14 6 0.19
15 15 0.48
16 1 0.03
17 4 0.13
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAAAATAATATTT
Found at i:6064 original size:30 final size:30
Alignment explanation
Indices: 6001--6087 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
5991 TTAATAATTC
* * * * * *
6001 TAATAAATAATAATTATATAAATATTATTT
1 TAATAAAAAATAACTATTTAAAAAATATAT
*
6031 TAATAAAAAAATAA-TATTTACAAAATATAT
1 TAAT-AAAAAATAACTATTTAAAAAATATAT
*
6061 TAATATAAAATAACTATTTAAAAAATA
1 TAATAAAAAATAACTATTTAAAAAATA
6088 CTAACATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
29 8 0.17
30 31 0.66
31 8 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
TAATAAAAAATAACTATTTAAAAAATATAT
Found at i:11531 original size:21 final size:21
Alignment explanation
Indices: 11505--11545 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
11495 GAGACAATTC
*
11505 TATGTGGTCATTTGGGACATA
1 TATGTGGTCATTTAGGACATA
11526 TATGTGGTCATTTAGGACAT
1 TATGTGGTCATTTAGGACAT
11546 TCTATGGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (21 bp):
TATGTGGTCATTTAGGACATA
Found at i:11571 original size:23 final size:24
Alignment explanation
Indices: 11545--11593 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
11535 ATTTAGGACA
*
11545 TTCTATG-GGCACTTCGGTGCATT
1 TTCTATGCGACACTTCGGTGCATT
*
11568 TTCTATGCGACACTTCGGTGTATT
1 TTCTATGCGACACTTCGGTGCATT
11592 TT
1 TT
11594 ATACGAGCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (24 bp):
TTCTATGCGACACTTCGGTGCATT
Found at i:15486 original size:20 final size:20
Alignment explanation
Indices: 15461--15773 Score: 256
Period size: 20 Copynumber: 15.4 Consensus size: 20
15451 ATTTTGCCAG
** *
15461 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
15481 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
15501 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* ** *
15520 CTATCGCAACTAGTATCCGTAAA
1 -AATCGCAACGCGAATCCGT--A
* *
15543 AATCACAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
15563 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
15584 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
15604 AATCGCAACGCGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
15624 AATCGCAACGCG-ATTCGGA
1 AATCGCAACGCGAATCCGTA
* * *
15643 ATATCGCAACGAGAATACGTT
1 A-ATCGCAACGCGAATCCGTA
* *
15664 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
15684 AATCGCAACGAGAATACGTAA
1 AATCGCAACGCGAATCCGT-A
* *
15705 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTA
*
15725 AATCGCAACGAGAATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
15745 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATCCGTA
15765 AATCGCAAC
1 AATCGCAAC
15774 ACTGAAATTT
Statistics
Matches: 240, Mismatches: 41, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
19 7 0.03
20 176 0.73
21 41 0.17
22 15 0.06
23 1 0.00
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:15726 original size:121 final size:122
Alignment explanation
Indices: 15461--15754 Score: 401
Period size: 121 Copynumber: 2.4 Consensus size: 122
15451 ATTTTGCCAG
* * * ** * *
15461 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCGATTCTGACTATCG
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAATACGTAAATCGCAACGCGATTCGGAATATCG
* * *
15526 CAACTAGTATCCGTAAAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAA
66 CAACGAGAATACGT-AAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAA
* *
15584 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACGTAAATCGCAACGCGATTCGGAATATCG
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAATACGTAAATCGCAACGCGATTCGGAATATCG
* * * *
15649 CAACGAGAATACGT-TAATCGCAATGCGTATCCGTAAATCGCAACGAGAATACGTAA
66 CAACGAGAATACGTAAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAA
* * *
15705 AATCGCAACGAGAATCTGTAAATCGCAACGAGAATCCGTAAATCGCAACG
1 AATCGCAACGCGAATCTGTAAATCGCAACGCGAATACGTAAATCGCAACG
15755 AGAATCTGTA
Statistics
Matches: 150, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
121 83 0.55
123 67 0.45
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.18
Consensus pattern (122 bp):
AATCGCAACGCGAATCTGTAAATCGCAACGCGAATACGTAAATCGCAACGCGATTCGGAATATCG
CAACGAGAATACGTAAAATCACAACGCGTATCCGTAAATCGCAACGACAATACGTAA
Found at i:16635 original size:24 final size:24
Alignment explanation
Indices: 16577--16623 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
16567 AGTCAGTATT
*
16577 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
16601 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
16624 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:19206 original size:33 final size:33
Alignment explanation
Indices: 19168--19349 Score: 213
Period size: 33 Copynumber: 5.3 Consensus size: 33
19158 CGAAAATTAC
19168 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* ** *
19201 AATCGCAACGTA-AAAATTACAACGCGAATATGAA
1 AATCGCAACG-AGAGAATCGCAATGCGAA-ATGAA
* *
19235 TATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAA
1 AATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATGAA
19274 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
19307 AATCGCAACGAGGGAATCGCAATGCGAAATTAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
19340 AATCGCAACG
1 AATCGCAACG
19350 CGAATTTAGT
Statistics
Matches: 127, Mismatches: 13, Indels: 18
0.80 0.08 0.11
Matches are distributed among these distances:
33 81 0.64
34 13 0.10
35 2 0.02
36 5 0.04
37 3 0.02
38 1 0.01
39 12 0.09
40 10 0.08
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:19245 original size:20 final size:19
Alignment explanation
Indices: 19183--19316 Score: 90
Period size: 19 Copynumber: 7.5 Consensus size: 19
19173 CAACGAGAGA
* *
19183 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
*
19202 ATCGCAACG-TAAA--AAT
1 ATCGCAACGCGAAATGAAT
*
19218 -T-ACAACGCGAATATGAAT
1 ATCGCAACGCGAA-ATGAAT
*
19236 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGAAT
* *
19256 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
*
19275 ATCGCAA--CGAGA-G-A-
1 ATCGCAACGCGAAATGAAT
* *
19289 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAT
19308 ATCGCAACG
1 ATCGCAACG
19317 AGGGAATCGC
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
14 12 0.13
15 4 0.04
16 8 0.09
17 5 0.06
18 7 0.08
19 31 0.34
20 20 0.22
21 3 0.03
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAT
Found at i:19272 original size:73 final size:66
Alignment explanation
Indices: 19154--19349 Score: 214
Period size: 73 Copynumber: 2.8 Consensus size: 66
19144 TGACTATCGT
* * *
19154 AACGCGAAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGTA-AAAAT
1 AACGCG-AAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG-AGAAAAT
*
19218 TAC
64 CAC
* *
19221 AACGCGAATATGAATATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAG
1 AACGCGAA-ATGAAAATCGCAACGAGG----GA--ATCGCAATGCGAAATGAAAATCGCAACGAG
* *
19286 AGAATCGC
59 AAAATCAC
* *
19294 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATTAAAATCGCAACG
1 AACGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG
19350 CGAATTTAGT
Statistics
Matches: 109, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
66 29 0.27
67 19 0.17
68 2 0.02
71 2 0.02
72 17 0.16
73 40 0.37
ACGTcount: A:0.44, C:0.19, G:0.21, T:0.15
Consensus pattern (66 bp):
AACGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCA
C
Found at i:19334 original size:106 final size:106
Alignment explanation
Indices: 19142--19351 Score: 289
Period size: 106 Copynumber: 2.0 Consensus size: 106
19132 CAATCATCTT
* * *
19142 AATGACTATCGTAACGCGAAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
* *
19207 AACGTAAAAATTACAACGCGAATATGAATATCGCAACGCGGA
66 AACGTAAAAATCACAACGCGAA-ATGAAAATCGCAACGCGGA
*
19249 AATGACTATCGCAATGCG-AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
1 AATGACTATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
** * * *
19313 AACG-AGGGAATCGCAATGCGAAATTAAAATCGCAACGCG
66 AACGTA-AAAATCACAACGCGAAATGAAAATCGCAACGCG
19352 AATTTAGTTT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 16 0.18
106 59 0.65
107 16 0.18
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (106 bp):
AATGACTATCGCAACGCGAAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGC
AACGTAAAAATCACAACGCGAAATGAAAATCGCAACGCGGA
Found at i:19403 original size:33 final size:33
Alignment explanation
Indices: 19359--19427 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
19349 GCGAATTTAG
* * *
19359 TTTCGCGTTGCGATTTTGTCATTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCATTGCGATTTTCA
**
19392 TTTCGCATTGCGATTCTCTTGTTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCATTGCGATTTTCA
19425 TTT
1 TTT
19428 TTGCCTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCATTGCGATTTTCA
Found at i:19545 original size:14 final size:14
Alignment explanation
Indices: 19526--19562 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
19516 CATCAATTAA
19526 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
19540 ACAAATCATCTTTT
1 ACAAATCAACTTTT
19554 ACAAATCAA
1 ACAAATCAA
19563 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:21001 original size:42 final size:42
Alignment explanation
Indices: 20955--21038 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
20945 TGATGACAGT
* *
20955 GGCCTCTTAAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTAAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * * *
20997 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTAAACGATAGGAGGGGACTCTCGAGGAATGATAGG
21039 CGAGTCGGGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTAAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:21914 original size:20 final size:20
Alignment explanation
Indices: 21886--21982 Score: 88
Period size: 20 Copynumber: 4.7 Consensus size: 20
21876 TGAAAATAAA
21886 ATACGCGTTGCGATTTACGG
1 ATACGCGTTGCGATTTACGG
* * *
21906 ATACACGTTGTGATTTTACGT
1 ATACGCGTTGCGA-TTTACGG
*
21927 AT-TGTCGTTGCGATTTACGG
1 ATACG-CGTTGCGATTTACGG
*
21947 ATACGCGTTGCAATTTTTACGG
1 ATACGCGTTGCGA--TTTACGG
**
21969 ATATTCGTTGCGAT
1 ATACGCGTTGCGAT
21983 AGTCAGAATC
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
20 27 0.45
21 16 0.27
22 17 0.28
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (20 bp):
ATACGCGTTGCGATTTACGG
Found at i:21948 original size:41 final size:42
Alignment explanation
Indices: 21891--21982 Score: 125
Period size: 41 Copynumber: 2.2 Consensus size: 42
21881 ATAAAATACG
** *
21891 CGTTGCGATTTACGGATACACGTTGTGA-TTTTACGTAT-TGT
1 CGTTGCGATTTACGGATACACGTTGCAATTTTTACGGATAT-T
*
21932 CGTTGCGATTTACGGATACGCGTTGCAATTTTTACGGATATT
1 CGTTGCGATTTACGGATACACGTTGCAATTTTTACGGATATT
21974 CGTTGCGAT
1 CGTTGCGAT
21983 AGTCAGAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
41 25 0.56
42 19 0.42
43 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (42 bp):
CGTTGCGATTTACGGATACACGTTGCAATTTTTACGGATATT
Found at i:22014 original size:20 final size:20
Alignment explanation
Indices: 21991--22043 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
21981 ATAGTCAGAA
*
21991 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
22011 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
22031 TCGCGTTGCGATT
1 TCGCGTTGCGATT
22044 CTGGCAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:25540 original size:59 final size:59
Alignment explanation
Indices: 25420--25551 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 59
25410 TTAATTGACT
* * *
25420 ATTTTATAACTTTTAATAGTCAATTGACTCAACAAAACAATATCATATAATTGAGAGATC
1 ATTTTGTAACTTTTAATAGTCAA-TGACTCAACAAAACAAAATCATATAATCGAGAGATC
* * *
25480 ATTTTGTAACTTTTAATAGTCAGA-GACTCAATAAAA-AACAATCTTATAATCGAGGGATC
1 ATTTTGTAACTTTTAATAGTCA-ATGACTCAACAAAACAA-AATCATATAATCGAGAGATC
25539 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
25552 ACCCTAATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
58 2 0.03
59 36 0.57
60 24 0.38
61 1 0.02
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.36
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCAATGACTCAACAAAACAAAATCATATAATCGAGAGATC
Found at i:33496 original size:20 final size:21
Alignment explanation
Indices: 33471--33522 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
33461 TTTTCCCAAT
*
33471 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
33491 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
33512 TCGCAATGCGA
1 TCGCAATGCGA
33523 TACTGACTAT
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:33536 original size:20 final size:20
Alignment explanation
Indices: 33511--33611 Score: 114
Period size: 20 Copynumber: 5.0 Consensus size: 20
33501 AATTGGGAAA
33511 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
33531 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
33551 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
33572 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
33592 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
33612 TTTGCAACGC
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 52 0.75
21 13 0.19
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:33555 original size:61 final size:61
Alignment explanation
Indices: 33508--33624 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
33498 GCGAATTGGG
* * * *
33508 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
33569 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTTGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
33625 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:33612 original size:20 final size:20
Alignment explanation
Indices: 33573--33625 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
33563 TAATACAAAA
* *
33573 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
33593 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
33613 TTGCAACGCGATT
1 TCGCAACGCGATT
33626 TACATAGCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:34204 original size:19 final size:19
Alignment explanation
Indices: 34168--34209 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
34158 AATTAACTAT
*
34168 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
* *
34187 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAA
34206 CGCA
1 CGCA
34210 TTGCGATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.29, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:34227 original size:19 final size:19
Alignment explanation
Indices: 34205--34349 Score: 148
Period size: 19 Copynumber: 8.1 Consensus size: 19
34195 GAAACCAAAA
*
34205 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
34224 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
34238 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
34257 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
34276 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
34290 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
34309 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
34328 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
34348 TC
1 TC
34350 AACCAAAAGA
Statistics
Matches: 105, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
14 20 0.19
16 5 0.05
17 6 0.06
19 57 0.54
20 17 0.16
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:34288 original size:52 final size:52
Alignment explanation
Indices: 34205--34341 Score: 220
Period size: 52 Copynumber: 2.6 Consensus size: 52
34195 GAAACCAAAA
* **
34205 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
34257 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
* *
34309 TCGCGTTGCGATTCTCATTATCTCGTTGCGATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATT
34342 TTCATTTCAA
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 67 0.85
53 12 0.15
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:34297 original size:33 final size:33
Alignment explanation
Indices: 34260--34324 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
34250 TTTCATTTCG
**
34260 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
34293 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCGCGTTGCGATTCTC
34325 ATTATCTCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.42
Consensus pattern (33 bp):
CGTTGCGATAGTCATTTCGCGTTGCGATTCTCT
Found at i:34818 original size:15 final size:15
Alignment explanation
Indices: 34798--34828 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34788 TAGGCCGGTA
34798 CACTCGTCATATCAC
1 CACTCGTCATATCAC
34813 CACTCGTCATATCAC
1 CACTCGTCATATCAC
34828 C
1 C
34829 CACCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.42, G:0.06, T:0.26
Consensus pattern (15 bp):
CACTCGTCATATCAC
Found at i:35916 original size:63 final size:63
Alignment explanation
Indices: 35817--35947 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
35807 GTTACGTGAT
35817 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
35880 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
1 GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
35943 GAGGT
1 GAGGT
35948 GTCTACTTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.24
Consensus pattern (63 bp):
GAGGTCAATGCCTTGCGTGAGGAGATCGGTACTCTACGCGATAACGATGGTGCATGGCGTGTG
Found at i:36596 original size:42 final size:42
Alignment explanation
Indices: 36520--36722 Score: 185
Period size: 42 Copynumber: 4.8 Consensus size: 42
36510 GACTCGCCTG
* * * * * * *
36520 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
36562 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * * * * * * * *
36604 TCATCCCTCAAGAATCCACTCCTATCATTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
36646 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
36688 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
36723 CCCGATTCAC
Statistics
Matches: 128, Mismatches: 31, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
41 4 0.03
42 122 0.95
43 2 0.02
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:36658 original size:84 final size:84
Alignment explanation
Indices: 36517--36692 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
36507 CCCGACTCGC
* *
36517 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAATCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
36582 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
36601 CTGTCATCCCTCAAGAATCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAATCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
36666 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
36685 CTGTCATC
1 CTGTCATC
36693 GTTGAAGAGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAATCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:36680 original size:21 final size:21
Alignment explanation
Indices: 36656--36722 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
36646 TCATTCCTCG
36656 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
36677 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
36698 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
36719 AGAG
1 AGAG
36723 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:36722 original size:84 final size:84
Alignment explanation
Indices: 36517--36722 Score: 288
Period size: 84 Copynumber: 2.5 Consensus size: 84
36507 CCCGACTCGC
* * * * *
36517 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAATCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
36582 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
* * *
36601 CTGTCATCCCTCAAGAATCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAATCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
36666 CCCACCGTTCAAGAGGCCA
66 CCCACCGTTCAAGAGGCCA
** * *
36685 CTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CTGTCATCCCTCAAGA-ATCCACTCCCACCATTCAAGAG
36723 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 109 0.97
85 3 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAATCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACCGTTCAAGAGGCCA
Found at i:38100 original size:14 final size:14
Alignment explanation
Indices: 38081--38116 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
38071 ATTGTTTAAT
38081 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
38095 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
38109 TGATTTGT
1 TGATTTGT
38117 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:38260 original size:14 final size:14
Alignment explanation
Indices: 38241--38297 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
38231 GCGAAATGAA
38241 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
38255 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
38274 AATCGCAACGAGAG
1 AATCGCAACGAGAG
38288 AATCGCAACG
1 AATCGCAACG
38298 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:38268 original size:33 final size:33
Alignment explanation
Indices: 38223--38312 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
38213 AAAAAGTACT
*
38223 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
38256 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
38289 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
38313 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:38282 original size:19 final size:19
Alignment explanation
Indices: 38223--38283 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
38213 AAAAAGTACT
*
38223 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
38242 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
38256 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
38275 ATCGCAACG
1 ATCGCAACG
38284 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:38330 original size:19 final size:19
Alignment explanation
Indices: 38308--38458 Score: 107
Period size: 19 Copynumber: 8.7 Consensus size: 19
38298 CGAAATTAAA
*
38308 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
38327 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
38343 TTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
38360 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
38374 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
38393 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
38408 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
** *
38426 TTCGCATTGCGATAGTAATT
1 TTCGCATTGCGATTTTCA-T
38446 TTCGCATTGCGAT
1 TTCGCATTGCGAT
38459 AGACATTAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 27 0.26
16 10 0.10
17 10 0.10
19 41 0.40
20 14 0.14
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:38354 original size:33 final size:32
Alignment explanation
Indices: 38312--38438 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
38302 ATTAAATTCG
38312 CGTTGCGATTTTCATTTCGCATTGCGATTCCTT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CTT
**
38345 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCTT
38378 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCT-T
*
38411 CATTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
38439 AGTAATTTTC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTT
Found at i:38390 original size:66 final size:66
Alignment explanation
Indices: 38305--38437 Score: 232
Period size: 66 Copynumber: 2.0 Consensus size: 66
38295 ACGCGAAATT
* *
38305 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTC-CTTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTC-TCATTGCGATTTTCATTTCGCATTG
38369 CG
65 CG
38371 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTTTCATTTCGCATTGC
38436 G
66 G
38437 A
1 A
38438 TAGTAATTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 63 0.98
67 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTTTCATTTCGCATTGC
G
Found at i:40747 original size:12 final size:12
Alignment explanation
Indices: 40730--40754 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40720 TCTTCGGGGA
40730 CTTTTTCTTCTT
1 CTTTTTCTTCTT
40742 CTTTTTCTTCTT
1 CTTTTTCTTCTT
40754 C
1 C
40755 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:42064 original size:20 final size:20
Alignment explanation
Indices: 42039--42096 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
42029 ATTCATTTGA
42039 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
42059 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
42079 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
42097 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:42156 original size:19 final size:19
Alignment explanation
Indices: 42115--42182 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
42105 GAAATGAAAA
42115 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
42131 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
42148 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
42167 TCGCATTGTGATTTTC
1 TCGCATTGCGATTTTC
42183 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:42201 original size:19 final size:19
Alignment explanation
Indices: 42179--42215 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42169 GCATTGTGAT
*
42179 TTTCTCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGTCA
42198 TTTCGCGTTGCGATAGTC
1 TTTCGCGTTGCGATAGTC
42216 TGTTTTGCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.41
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTCA
Found at i:44227 original size:20 final size:19
Alignment explanation
Indices: 44204--44299 Score: 78
Period size: 20 Copynumber: 5.3 Consensus size: 19
44194 CTTAAAATCA
44204 CAACGCGAAAATGACTATCG
1 CAACGCG-AAATGACTATCG
*
44224 CAACGCGGAAATGGCTATCG
1 CAACGC-GAAATGACTATCG
* **
44244 CAATGCGAAATGAAAATCG
1 CAACGCGAAATGACTATCG
*
44263 CAA--CGAAA--A-AATCG
1 CAACGCGAAATGACTATCG
*
44277 CAACGCGAAATGA-AATCG
1 CAACGCGAAATGACTATCG
44295 CAACG
1 CAACG
44300 ACAAAATCGC
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
14 8 0.12
15 1 0.02
16 5 0.08
17 5 0.08
18 11 0.17
19 13 0.20
20 22 0.33
21 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
CAACGCGAAATGACTATCG
Found at i:44275 original size:14 final size:14
Alignment explanation
Indices: 44256--44313 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
44246 ATGCGAAATG
44256 AAAATCGCAACGAA
1 AAAATCGCAACGAA
44270 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
*
44286 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAA
44302 AAAATCGCAACG
1 AAAATCGCAACG
44314 CGAAACACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:44298 original size:32 final size:33
Alignment explanation
Indices: 44240--44318 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
44230 GGAAATGGCT
*
44240 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
*
44273 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
44305 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
44319 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
Found at i:44366 original size:14 final size:14
Alignment explanation
Indices: 44347--44404 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
44337 TTTCATTTCG
44347 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
44361 CGTTGCGATTTTATTT
1 CGTTGCGA-TTT-TGT
44377 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
44393 CGTTGCGATTTT
1 CGTTGCGATTTT
44405 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.53
15 3 0.08
16 4 0.11
17 3 0.08
18 8 0.21
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:44382 original size:32 final size:33
Alignment explanation
Indices: 44330--44420 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
44320 ACAAATCGCA
44330 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
44363 TTGCGATTTT-ATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
44395 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
44421 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:44427 original size:19 final size:20
Alignment explanation
Indices: 44405--44448 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
44395 TTGCGATTTT
44405 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
44424 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
44444 CATTT
1 CATTT
44449 TCATGTTGCG
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):
CATTTCCGCATTGCGATAGC
Found at i:44456 original size:20 final size:20
Alignment explanation
Indices: 44414--44459 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
44404 TCATTTCGCA
*
44414 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCACG
* * *
44434 TTGCGATAGTCATTTTCATG
1 TTGCGATAGCCATTTCCACG
44454 TTGCGA
1 TTGCGA
44460 AAGTAAACTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCACG
Found at i:44961 original size:18 final size:18
Alignment explanation
Indices: 44935--44979 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
44925 GTCGATCAGA
*
44935 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
44953 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
44971 TGATGGCTC
1 TGATGGCTC
44980 CCAAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:46347 original size:20 final size:20
Alignment explanation
Indices: 46299--46357 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
46289 AATAGTTTCT
** *
46299 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
46319 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
** *
46339 GAATTTGACTATCACAACG
1 GAAAATGACTATCGCAACG
46358 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:46645 original size:22 final size:22
Alignment explanation
Indices: 46620--46663 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
46610 GATGAAGATA
*
46620 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
46642 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
46664 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:46877 original size:20 final size:20
Alignment explanation
Indices: 46851--46923 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
46841 GATTATGTAT
46851 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
46871 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
46891 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
46911 TATCTCGTTGCGA
1 TATCGCGTTGCGA
46924 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:46954 original size:41 final size:41
Alignment explanation
Indices: 46831--46966 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
46821 CGCTTTGAAA
* *
46831 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * *
46872 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
46912 ATCTCGTTGCGATTTTGTATTATCGCATTGTGATAGTCAGT
1 ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* *
46953 ATGGCATTGCGATT
1 ATCGCGTTGCGATT
46967 TTCCCAATTC
Statistics
Matches: 76, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.41
41 40 0.53
42 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
ATCGCGTTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:46985 original size:21 final size:21
Alignment explanation
Indices: 46959--47029 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
46949 CAGTATGGCA
46959 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
* ** *
46980 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCGCG
47000 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTTCCCAATTCGCG
47021 TTGCGATTT
1 TTGCGATTT
47030 ACTTATTCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.42
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCGCG
Found at i:46998 original size:20 final size:20
Alignment explanation
Indices: 46973--47046 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
46963 GATTTTCCCA
*
46973 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
* **
46993 ATTCGCATTGCGATTTTCCCA
1 ATTCGCATTGCGA-TTTACTT
*
47014 ATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
47034 ATTCGCATTGCGA
1 ATTCGCATTGCGA
47047 ATTTGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:47001 original size:41 final size:41
Alignment explanation
Indices: 46956--47046 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
46946 AGTCAGTATG
46956 GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
1 GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
46997 GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
1 GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
47038 GCATTGCGA
1 GCATTGCGA
47047 ATTTGGAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.40
Consensus pattern (41 bp):
GCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTC
Found at i:47866 original size:13 final size:13
Alignment explanation
Indices: 47848--47873 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47838 CGATGGGTTT
47848 TTAAATAAATAAA
1 TTAAATAAATAAA
47861 TTAAATAAATAAA
1 TTAAATAAATAAA
47874 GGCTAAGAGA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TTAAATAAATAAA
Found at i:49192 original size:33 final size:32
Alignment explanation
Indices: 49146--49210 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
49136 TTAAGTCATG
* *
49146 TAAGGAAAATGTCTCAATTGAGACAAATTTTT
1 TAAGGAAAATGTCTCAAGTGAGACAAAGTTTT
*
49178 TAAGTGAAAATGTCTCAAGTGAGATAAAGTTTT
1 TAAG-GAAAATGTCTCAAGTGAGACAAAGTTTT
49211 ATTTAGAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (32 bp):
TAAGGAAAATGTCTCAAGTGAGACAAAGTTTT
Found at i:49344 original size:71 final size:70
Alignment explanation
Indices: 49183--49809 Score: 585
Period size: 71 Copynumber: 8.9 Consensus size: 70
49173 TTTTTTAAGT
* * * * * * * *
49183 GAAAATGTCTCAAGTGAGAT-AAAGTTTTATTTAGAGAGAAATTGTATTGAGTGTGATGAAAATT
1 GAAAATATCTCAAGTGAGATGAAA-TTTTGTTTA-AGAGAAACTGTCTCGAGTGAGATAAAAAAT
49247 TTCCAAGG
64 TT-CAAGG
* * *
49255 GAAAATATCTCATGTGAGATGAAATTTTGTTTCAAGAGAAATTGTCTCGAGTGAGACAAAAAATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTT-AAGAGAAACTGTCTCGAGTGAGATAAAAAATT
49320 TCAAGG
65 TCAAGG
* * * ** *
49326 GAAAATATCTCAAGTGAGACGAAGTTTTATTTCAAGAGAAACTGTCTCGA--GAG--ACGAATTT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTT-AAGAGAAACTGTCTCGAGTGAGATAAAAAATT
49387 TCAAGG
65 TCAAGG
* * * * * * * * *
49393 GAAAATATTTCAACTAAGATAAAATTTTGTTTCGAGATAAACTGTCTTGAGTGAGACAAAAATTT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTT-AAGAGAAACTGTCTCGAGTGAGATAAAAAATT
49458 TCAAGG
65 TCAAGG
* * * *
49464 GAAAATATCTCAAGTGAGATGAAATTTTGTTATGAGAGAAACTGTCTCGACTAAGATGAAAAATT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTT-TAAGAGAAACTGTCTCGAGTGAGATAAAAAATT
49529 TCATA-G
65 TCA-AGG
* * * * * *
49535 GAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAAGTATCTCGAGTGAGATGAAAACTT
1 GAAAATATCTCAAGTGAGATGAAATTTTG-TTTAAGAGAAACTGTCTCGAGTGAGATAAAAAATT
49600 TCACA-G
65 TCA-AGG
* * * * *
49606 GAAAGTATCTCAAGTGAGATGAAAATTTGTTTTTAGAGAAACTGTCTCGAGTGAGA-CAGAAA-T
1 GAAAATATCTCAAGTGAGATGAAATTTTG-TTTAAGAGAAACTGTCTCGAGTGAGATAAAAAATT
*
49669 T-AAAG
65 TCAAGG
* * *
49674 GAAAATATCTCAAGTGAGATGAAATTTTATTTAGAGAGAAAC--TCTCGAGTGAGATAGAAATTT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTA-AGAGAAACTGTCTCGAGTGAGATAAAAAATT
49737 TCAAGG
65 TCAAGG
* ** * * *
49743 GAAAATATCTCAAGTGAGATGATATTTTGTTTGTGAGGAAAATTATCTCAAGTGAGATAAAAAAT
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTAAGA-G-AAACTGTCTCGAGTGAGATAAAAAAT
49808 TT
64 TT
49810 GTTTCAAGAA
Statistics
Matches: 464, Mismatches: 73, Indels: 36
0.81 0.13 0.06
Matches are distributed among these distances:
66 12 0.03
67 57 0.12
68 40 0.09
69 42 0.09
70 6 0.01
71 229 0.49
72 74 0.16
73 4 0.01
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.30
Consensus pattern (70 bp):
GAAAATATCTCAAGTGAGATGAAATTTTGTTTAAGAGAAACTGTCTCGAGTGAGATAAAAAATTT
CAAGG
Found at i:49361 original size:37 final size:36
Alignment explanation
Indices: 49250--49387 Score: 104
Period size: 37 Copynumber: 3.9 Consensus size: 36
49240 GAAAATTTTC
* * * *
49250 CAAGGGAAAATATCTCATGTGAGATGAAATTTTGTTT
1 CAAGAGAAAATATCTCAAGTGAGACG-AATTTTATTT
* * * ***
49287 CAAGAGAAATTGTCTCGAGTGAGAC-AA-AAAATTT
1 CAAGAGAAAATATCTCAAGTGAGACGAATTTTATTT
*
49321 CAAGGGAAAATATCTCAAGTGAGACGAAGTTTTATTT
1 CAAGAGAAAATATCTCAAGTGAGACGAA-TTTTATTT
* * *
49358 CAAGAGAAACTGTCTC--GAGAGACGAATTTT
1 CAAGAGAAAATATCTCAAGTGAGACGAATTTT
49388 CAAGGGAAAA
Statistics
Matches: 77, Mismatches: 21, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
34 28 0.36
35 13 0.17
37 36 0.47
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (36 bp):
CAAGAGAAAATATCTCAAGTGAGACGAATTTTATTT
Found at i:49558 original size:34 final size:34
Alignment explanation
Indices: 49442--49630 Score: 121
Period size: 34 Copynumber: 5.4 Consensus size: 34
49432 AACTGTCTTG
* *
49442 AGTGAGA-CAAAAATTTTCA-AGGGAAAATATCTCA
1 AGTGAGATGAAAAA-TTTCATA-GGAAAGTATCTCA
** * * * *
49476 AGTGAGATGAAATTTTGTTATGAGAGAAACTGTCTCG
1 AGTGAGATGAAAAATT-TCAT-AG-GAAAGTATCTCA
* * * *
49513 ACTAAGATGAAAAATTTCATAGGAAAATACCTCA
1 AGTGAGATGAAAAATTTCATAGGAAAGTATCTCA
** ** *
49547 AGTGAGATGAAATTTTGTTTTGAGAGAAAGTATCTCG
1 AGTGAGATGAAAAATT-TCAT-AG-GAAAGTATCTCA
* *
49584 AGTGAGATGAAAACTTTCACAGGAAAGTATCTCA
1 AGTGAGATGAAAAATTTCATAGGAAAGTATCTCA
49618 AGTGAGATGAAAA
1 AGTGAGATGAAAA
49631 TTTGTTTTTA
Statistics
Matches: 116, Mismatches: 31, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
34 53 0.46
35 11 0.09
36 7 0.06
37 45 0.39
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (34 bp):
AGTGAGATGAAAAATTTCATAGGAAAGTATCTCA
Found at i:49575 original size:209 final size:210
Alignment explanation
Indices: 49183--49783 Score: 652
Period size: 209 Copynumber: 2.9 Consensus size: 210
49173 TTTTTTAAGT
* * * * * * * * **
49183 GAAAATGTCTCAAGTGAGATAAAGTTTTATTTAGAGAGAAATTGTATTGAGTGTGATGAAAATTT
1 GAAAATATCTCAACTAAGATAAAATTTTGTTTAGAGAGAAACTGTCTTGAGTGAGACAAAAATTT
* *
49248 TCCAAGGGAAAATATCTCATGTGAGATGAAATTTTGTTTCA-AGAGAAATTGTCTCGAGTGAGAC
66 T-CAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTT-AGAGAGAAACTGTCTCGAGTGAGA-
* * * * ** *
49312 AAAAAATTTCAAGGGAAAATATCTCAAGTGAGACGAAGTTTTATTTCAAGAGAAACTGTCTCGA-
128 TAAAAATTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAACTATCTCGAG
*
49376 GAGACG-AATTTTCA-AGG
193 GAGACGAAACTTTCACA-G
* * *
49393 GAAAATATTTCAACTAAGATAAAATTTTGTTTCGAGATAAACTGTCTTGAGTGAGACAAAAATTT
1 GAAAATATCTCAACTAAGATAAAATTTTGTTTAGAGAGAAACTGTCTTGAGTGAGACAAAAATTT
* *
49458 TCAAGGGAAAATATCTCAAGTGAGATGAAATTTTG-TTATGAGAGAAACTGTCTCGACTAAGATG
66 TCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTA-GAGAGAAACTGTCTCGAGTGAGAT-
* *
49522 AAAAATTTCATA-GGAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAAGTATCTCGAG
129 AAAAATTTCA-AGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAACTATCTCGAG
*
49586 TGAGATGAAAACTTTCACAG
193 -GAGACG-AAACTTTCACAG
* * * ** * *
49606 GAAAGTATCTCAAGTGAGATGAAAA-TTTGTTTTTAGAGAAACTGTCTCGAGTGAGACAGAAA--
1 GAAAATATCTCAACTAAGAT-AAAATTTTGTTTAGAGAGAAACTGTCTTGAGTGAGACAAAAATT
* *
49668 TT-AAAGGAAAATATCTCAAGTGAGATGAAATTTTATTTAGAGAGAAAC--TCTCGAGTGAGATA
65 TTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTAGAGAGAAACTGTCTCGAGTGAGATA
* *
49730 GAAATTTTCAAGGGAAAATATCTCAAGTGAGATGATATTTTGTTTGTGAG-GAAA
130 -AAAATTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTT-TGAGAGAAA
49784 ATTATCTCAA
Statistics
Matches: 333, Mismatches: 44, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
207 3 0.01
208 56 0.17
209 109 0.33
210 94 0.28
211 10 0.03
213 56 0.17
214 5 0.02
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (210 bp):
GAAAATATCTCAACTAAGATAAAATTTTGTTTAGAGAGAAACTGTCTTGAGTGAGACAAAAATTT
TCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTAGAGAGAAACTGTCTCGAGTGAGATAA
AAATTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAACTATCTCGAGGAG
ACGAAACTTTCACAG
Found at i:49591 original size:37 final size:37
Alignment explanation
Indices: 49464--49800 Score: 183
Period size: 37 Copynumber: 9.5 Consensus size: 37
49454 ATTTTCAAGG
*
49464 GAAAATATCTCAAGTGAGATGAAATTTTGTTATGAGA
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGA
* * * * * ** **
49501 GAAACTGTCTCGACTAAGATGAAAAATT-TCAT-AG-
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGA
*
49535 GAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGA
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGA
* * ** ***
49572 GAAAGTATCTCGAGTGAGATGAAA-ACT-TTCACAG-
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGA
* * *
49606 GAAAGTATCTCAAGTGAGATGAAAATTTGTTTTTAGA
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGA
* * * * **
49643 GAAACTGTCTCGAGTGAGACAGAAA------TTAAAG-
1 GAAAATATCTCAAGTGAGA-TGAAATTTTGTTTTGAGA
* *
49674 GAAAATATCTCAAGTGAGATGAAATTTTATTTAGAGA
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGA
* * ** *
49711 G-AAA-CTCTCGAGTGAGATAGAAA---T-TTTCAAGG
1 GAAAATATCTCAAGTGAGAT-GAAATTTTGTTTTGAGA
*
49743 GAAAATATCTCAAGTGAGATGATATTTTGTTTGTGAG-
1 GAAAATATCTCAAGTGAGATGAAATTTTGTTT-TGAGA
49780 GAAAATTATCTCAAGTGAGAT
1 GAAAA-TATCTCAAGTGAGAT
49801 AAAAAATTTG
Statistics
Matches: 224, Mismatches: 53, Indels: 45
0.70 0.16 0.14
Matches are distributed among these distances:
30 4 0.02
31 16 0.07
32 10 0.04
33 7 0.03
34 55 0.25
35 21 0.09
36 23 0.10
37 67 0.30
38 21 0.09
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (37 bp):
GAAAATATCTCAAGTGAGATGAAATTTTGTTTTGAGA
Found at i:49808 original size:280 final size:279
Alignment explanation
Indices: 49254--49809 Score: 690
Period size: 280 Copynumber: 2.0 Consensus size: 279
49244 ATTTTCCAAG
* * * *
49254 GGAAAATATCTCATGTGAGATGAAATTTTGTTTCAAGAGAAATTGTCTCGAGTGAGACAAAAAAT
1 GGAAAATACCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAAGTATCTCGAGTGAGACAAAAAAT
**
49319 TTCAAGGGAAAATATCTCAAGTGAGACGAAGTTTTATTTCAAGAGAAACTGTCTCGAGAGACGAA
66 TTCAAGGGAAAATATCTCAAGTGAGACGAAAATTTATTTCAAGAGAAACTGTCTCGAGAGACGAA
* * * * * * *
49384 TTTTCAAGGGAAAATATTTCAACTAAGATAAAATTTTGTTTCGAGATAAACTGTCTTGAGTGAGA
131 TATTCAAAGGAAAATATCTCAACTAAGATAAAATTTTATTTAGAGAGAAAC-GTCTCGAGTGAGA
* *
49449 CAAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTATGAGAGAAACTGTCTCGA
195 CAAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTATGAGAGAAACTATCTCAA
*
49514 CTAAGATGAAAAATTTCATA
260 CTAAGATAAAAAATTTCATA
** ** *
49534 GGAAAATACCTCAAGTGAGATGAAATTTTGTTTTGAGAGAAAGTATCTCGAGTGAGATGAAAACT
1 GGAAAATACCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAAGTATCTCGAGTGAGACAAAAAAT
* * * **
49599 TTCACA-GGAAAGTATCTCAAGTGAGATGAAAATTTGTTTTTAGAGAAACTGTCTCGAGTGAGAC
66 TTCA-AGGGAAAATATCTCAAGTGAGACGAAAATTTATTTCAAGAGAAACTGTCTCGA--GAGAC
* * *
49663 AGAA-ATT-AAAGGAAAATATCTCAAGTGAGATGAAATTTTATTTAGAGAGAAAC-TCTCGAGTG
128 -GAATATTCAAAGGAAAATATCTCAACTAAGATAAAATTTTATTTAGAGAGAAACGTCTCGAGTG
* * * * *
49725 AGATAGAAATTTTCAAGGGAAAATATCTCAAGTGAGATGATATTTTGTT-TGTGAGGAAAATTAT
192 AGACAAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTATGAGA-G-AAACTAT
* *
49789 CTCAAGTGAGATAAAAAATTT
255 CTCAACTAAGATAAAAAATTT
49810 GTTTCAAGAA
Statistics
Matches: 234, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
278 4 0.02
279 55 0.24
280 126 0.54
281 39 0.17
282 7 0.03
283 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.30
Consensus pattern (279 bp):
GGAAAATACCTCAAGTGAGATGAAATTTTGTTTCAAGAGAAAGTATCTCGAGTGAGACAAAAAAT
TTCAAGGGAAAATATCTCAAGTGAGACGAAAATTTATTTCAAGAGAAACTGTCTCGAGAGACGAA
TATTCAAAGGAAAATATCTCAACTAAGATAAAATTTTATTTAGAGAGAAACGTCTCGAGTGAGAC
AAAAATTTTCAAGGGAAAATATCTCAAGTGAGATGAAATTTTGTTATGAGAGAAACTATCTCAAC
TAAGATAAAAAATTTCATA
Found at i:50199 original size:46 final size:46
Alignment explanation
Indices: 50102--50199 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 46
50092 CAAGAGAGGA
** * *
50102 AAAAATGATCTTAAGAAAAACAAATTTGAAAGTATTCTCATGGGAG
1 AAAAATGATCTTAAGAAAAACAAAAATGAAAGTATCCTCATGAGAG
*
50148 AAAAATGATCTTAAGAAACAA-AAAAATGAGAA-TATCCTCGTGAGAG
1 AAAAATGATCTTAAGAAA-AACAAAAATGA-AAGTATCCTCATGAGAG
*
50194 GAAAAT
1 AAAAAT
50200 AATGAATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
46 40 0.91
47 4 0.09
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.22
Consensus pattern (46 bp):
AAAAATGATCTTAAGAAAAACAAAAATGAAAGTATCCTCATGAGAG
Found at i:56838 original size:138 final size:139
Alignment explanation
Indices: 56669--56918 Score: 344
Period size: 138 Copynumber: 1.8 Consensus size: 139
56659 TTATAAGCTA
* * * * * *
56669 TAATATTAACCATAATTGATTTTAACTAATTATTGGATCGAATAATCGAAATGGACCCTTGGGCA
1 TAATATTAACCATAATTGATTTTAACCAATTATTGAATCGAATAACCAAAATGGACCATCGGG-A
* * * * *
56734 -TTAAGGCGAGGGTCAGATCAAATATTCCCTA-AATTAAGGGACTAAAGTGAAACTTAGCCTAAA
65 GTTAAGGCGAGAGCCAAATCAAATATTCCCTACAATTAAAGAACTAAAGTGAAACTTAGCCTAAA
56797 ATGGAGGCTC
130 ATGGAGGCTC
56807 TAATATTAATCC-TAATTGATTTTAACCAATTATTGAATCGAATAACCAAAATGGACCATCGGGA
1 TAATATTAA-CCATAATTGATTTTAACCAATTATTGAATCGAATAACCAAAATGGACCATCGGGA
**
56871 GTTAAGGCGAGAGCCAAATTGAATATTCCCTACAATTAAAGAACTAAA
65 GTTAAGGCGAGAGCCAAATCAAATATTCCCTACAATTAAAGAACTAAA
56919 AGTTTAGAGA
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
137 1 0.01
138 80 0.83
139 15 0.16
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (139 bp):
TAATATTAACCATAATTGATTTTAACCAATTATTGAATCGAATAACCAAAATGGACCATCGGGAG
TTAAGGCGAGAGCCAAATCAAATATTCCCTACAATTAAAGAACTAAAGTGAAACTTAGCCTAAAA
TGGAGGCTC
Found at i:59003 original size:21 final size:22
Alignment explanation
Indices: 58978--59020 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
58968 TCCAGATTGT
58978 CCAAA-GGGAACCGATTCCCCC
1 CCAAAGGGGAACCGATTCCCCC
*
58999 CCAAAGGGGTACCGATTCCCCC
1 CCAAAGGGGAACCGATTCCCCC
59021 TGAATGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.26, C:0.42, G:0.21, T:0.12
Consensus pattern (22 bp):
CCAAAGGGGAACCGATTCCCCC
Done.