Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001998.1 Hibiscus syriacus cultivar Beakdansim tig00004089_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: 118633
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2645 original size:21 final size:20
Alignment explanation
Indices: 2619--2662 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
2609 GATTTCTGGG
* *
2619 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
2640 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
2660 CAA
1 CAA
2663 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:3300 original size:23 final size:24
Alignment explanation
Indices: 3257--3303 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
3247 ATATGGCATG
*
3257 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
3281 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
3304 ACAAGTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:3519 original size:31 final size:31
Alignment explanation
Indices: 3481--3598 Score: 191
Period size: 31 Copynumber: 3.8 Consensus size: 31
3471 AGGGTGGAGG
*
3481 GTTTACCTATGTTCTTCTGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
3512 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3543 GATTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3574 GTTTACCTATGTCCTTCGGGACATA
1 GTTTACCTATGTTCTTCGGGACATA
3599 CTGATTACCT
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 80 1.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:3631 original size:58 final size:60
Alignment explanation
Indices: 3483--3632 Score: 209
Period size: 62 Copynumber: 2.5 Consensus size: 60
3473 GGTGGAGGGT
*
3483 TTACCTATGTTCTTCTGG-ACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTC-GGAACATATGGACTGTTTACCTATGTCCTTCGGGACA-AT-GACTGA
*
3545 TTACCTATGTTCTTCGGAACATACGGACTGTTTACCTATGTCCTTCGGGAC-AT-ACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACAATGACTGA
*
3603 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
3633 GTCCTTCGGG
Statistics
Matches: 82, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
58 31 0.38
59 1 0.01
60 2 0.02
61 2 0.02
62 46 0.56
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (60 bp):
TTACCTATGTTCTTCGGAACATATGGACTGTTTACCTATGTCCTTCGGGACAATGACTGA
Found at i:7179 original size:23 final size:24
Alignment explanation
Indices: 7136--7182 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
7126 ATATGGCATG
*
7136 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
7160 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
7183 ACAAGTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:7412 original size:31 final size:31
Alignment explanation
Indices: 7359--7507 Score: 170
Period size: 31 Copynumber: 5.0 Consensus size: 31
7349 AGGGTGGAGG
7359 GTTTACCTATGTTC-T--GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
7387 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
7418 GATTACCTA-G---TTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
7445 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
7476 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
7507 G
1 G
7508 GTCCTTCGGG
Statistics
Matches: 103, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
27 23 0.22
28 15 0.15
29 1 0.01
30 1 0.01
31 62 0.60
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:7452 original size:58 final size:58
Alignment explanation
Indices: 7361--7490 Score: 208
Period size: 58 Copynumber: 2.2 Consensus size: 58
7351 GGTGGAGGGT
* *
7361 TTACCTATGTTCTGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTA-GTTCTGGACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
7420 TTACCTAGTTC-GGAACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTAGTTCTGG-ACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
7478 TTACCTAGGTTCT
1 TTACCTA-GTTCT
7491 TCGGAATCTA
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
57 2 0.03
58 53 0.80
59 11 0.17
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (58 bp):
TTACCTAGTTCTGGACATACGGACTGTTTACCTATGTCCTTCGGGACATATGGACTGA
Found at i:11178 original size:11 final size:11
Alignment explanation
Indices: 11162--11218 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
11152 TTGTACTCAA
11162 ATTAAATAAAT
1 ATTAAATAAAT
11173 ATTAAA-AAATT
1 ATTAAATAAA-T
11184 ATTTAAATAAAT
1 A-TTAAATAAAT
*
11196 -TTTAAT-AAT
1 ATTAAATAAAT
11205 ATTATAA-AAAT
1 ATTA-AATAAAT
11216 ATT
1 ATT
11219 TTATAACCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
9 3 0.08
10 10 0.26
11 16 0.42
12 6 0.16
13 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATTAAATAAAT
Found at i:11189 original size:23 final size:24
Alignment explanation
Indices: 11163--11209 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
11153 TGTACTCAAA
11163 TTAAATAAATATTAA-AAAATTAT
1 TTAAATAAATATTAATAAAATTAT
* *
11186 TTAAATAAATTTTAATAATATTAT
1 TTAAATAAATATTAATAAAATTAT
11210 AAAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAAATAAATATTAATAAAATTAT
Found at i:19260 original size:21 final size:21
Alignment explanation
Indices: 19225--19265 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
19215 TTAAAACAGT
19225 TTTTTAATAACTTAAATAATTA
1 TTTTTAATAACTTAAA-AATTA
*
19247 TTTTTAATCA-TTAAAAATT
1 TTTTTAATAACTTAAAAATT
19266 TCTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 5 0.28
22 9 0.50
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTTAATAACTTAAAAATTA
Found at i:21801 original size:14 final size:15
Alignment explanation
Indices: 21770--21801 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
21760 AATATCTTTT
21770 AAAATAATTTTAAGA
1 AAAATAATTTTAAGA
21785 AAAATAATTTTAA-A
1 AAAATAATTTTAAGA
21799 AAA
1 AAA
21802 CAAAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
AAAATAATTTTAAGA
Found at i:23970 original size:3 final size:3
Alignment explanation
Indices: 23956--24000 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
23946 TTTGGGCTTG
*
23956 TAA TAA -AA TAA TAA TAA TAA TAA TAAA TAT TAAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TA
24001 TAAATAATCC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.81
4 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25118 original size:97 final size:100
Alignment explanation
Indices: 24953--25184 Score: 285
Period size: 97 Copynumber: 2.3 Consensus size: 100
24943 TAAAAAAATA
* * *
24953 TAGCACTTAACACATACTTACACCGGTATAAGTGAATAAAATAAACAAGTGTAGCACTTAACATA
1 TAGCACTTAACACATAC-TACACCGGTATAAGTGAAT-AAATAAACAAGTATAACACTTAACACA
* * *
25018 TACTTACACCT-ATGTAAGTGAATAAAACAAAAAGAGTG
64 TACTTACA-ATGATGTAAGTAAATAAAACAAAAA-AGCG
* *
25056 TAGCACTTAACACATACTATACCGGTGTAAGTGAAT-AA-AAA-AA-TATAACACTTAACACATA
1 TAGCACTTAACACATACTACACCGGTATAAGTGAATAAATAAACAAGTATAACACTTAACACATA
* *
25117 CTTACAATGGTGTAAGTAAATAAAATAAAAAAGCG
66 CTTACAATGATGTAAGTAAATAAAACAAAAAAGCG
*
25152 TAGCACTTAACACATACTTACACCGATATAAGT
1 TAGCACTTAACACATAC-TACACCGGTATAAGT
25185 ATGTACATAT
Statistics
Matches: 114, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
96 21 0.18
97 52 0.46
98 2 0.02
99 3 0.03
100 2 0.02
102 17 0.15
103 17 0.15
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (100 bp):
TAGCACTTAACACATACTACACCGGTATAAGTGAATAAATAAACAAGTATAACACTTAACACATA
CTTACAATGATGTAAGTAAATAAAACAAAAAAGCG
Found at i:25185 original size:51 final size:51
Alignment explanation
Indices: 24943--25176 Score: 282
Period size: 51 Copynumber: 4.7 Consensus size: 51
24933 TAATTCATAC
* * *
24943 TAAAAAAATATAGCACTTAACACATACTTACACCGGTATAAGTGAATAAAA
1 TAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAA
* * **
24994 TAAACAAGTGTAGCACTTAACATATACTTACACCTATGTAAGTGAATAAAA
1 TAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAA
* *
25045 CAAAAAGAGTGTAGCACTTAACACATAC-TATACCGGTGTAAGTGAAT---A
1 TAAAAA-AGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAA
* * ** *
25093 -AAAAAA-TATAACACTTAACACATACTTACAATGGTGTAAGTAAATAAAA
1 TAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAA
*
25142 TAAAAAAGCGTAGCACTTAACACATACTTACACCG
1 TAAAAAAGTGTAGCACTTAACACATACTTACACCG
25177 ATATAAGTAT
Statistics
Matches: 152, Mismatches: 24, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
45 17 0.11
46 16 0.11
47 5 0.03
48 1 0.01
49 1 0.01
50 6 0.04
51 86 0.57
52 20 0.13
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (51 bp):
TAAAAAAGTGTAGCACTTAACACATACTTACACCGGTGTAAGTGAATAAAA
Found at i:26425 original size:2 final size:2
Alignment explanation
Indices: 26418--26454 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
26408 ATAATTAAAT
26418 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26455 GATAAATTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29623 original size:60 final size:61
Alignment explanation
Indices: 29505--29633 Score: 156
Period size: 60 Copynumber: 2.1 Consensus size: 61
29495 TCCTCATTTC
* **
29505 AAATTAGT-TCTTAAACTTTTAAAAATTCCAATTTCATCCCAAAACTAAGACTTTCATTCT
1 AAATTAGTCTCTTAAACTTTTAAAAATTCCAATTTCATCCCAAAACTAAGAATAACATTCT
* * * *
29565 AAATTAGTCT-TTAAACTTTTGAACATTCTAATTTCATACCC-AAACTATGAATAACATTCT
1 AAATTAGTCTCTTAAACTTTTAAAAATTCCAATTTCAT-CCCAAAACTAAGAATAACATTCT
*
29625 AAATAAGTC
1 AAATTAGTC
29634 CCTAATCTTG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
60 55 0.93
61 4 0.07
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (61 bp):
AAATTAGTCTCTTAAACTTTTAAAAATTCCAATTTCATCCCAAAACTAAGAATAACATTCT
Found at i:29929 original size:58 final size:58
Alignment explanation
Indices: 29805--29947 Score: 139
Period size: 58 Copynumber: 2.4 Consensus size: 58
29795 ATTTAGCATT
**
29805 AAATTGAGATGTTCAAAAAGTTTAGAGACCAATTTAGAATAAAGATCAAGTTTGGGGATGA
1 AAATTGA-ATGTT--AAAAGTTTAGAGACCAATTTAGAATAAAGATCAAGTTTAAGGATGA
* *
29866 AAATTGAATGTTAAAAGTTT-GAGGACTAATTTAGAATGATAG-TCATAGTTTAAGGATG-
1 AAATTGAATGTTAAAAGTTTAGA-GACCAATTTAGAAT-AAAGATCA-AGTTTAAGGATGA
* *
29924 GAATTGGAATGTTTAGAAGTTTAG
1 AAATT-GAATG-TTAAAAGTTTAG
29948 GGATTAATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 12
0.80 0.07 0.14
Matches are distributed among these distances:
57 2 0.03
58 28 0.40
59 18 0.26
60 14 0.20
61 8 0.11
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (58 bp):
AAATTGAATGTTAAAAGTTTAGAGACCAATTTAGAATAAAGATCAAGTTTAAGGATGA
Found at i:36812 original size:136 final size:136
Alignment explanation
Indices: 36617--36883 Score: 399
Period size: 136 Copynumber: 2.0 Consensus size: 136
36607 TCATTGTGGT
*
36617 TCTCGTGCGAGTCTCTCTAATTCATCGGGACTTCCATGTGAGTCACCTAGAATAATATGATTAGG
1 TCTCGTGCGAGTCTCTCTAATTCATCGGGACTTCCATGTGAGTCACCCAGAATAATATGATTAGG
** * * * * * *
36682 TGCTTCTGTACGAGTTACTCTAATTCATTGTGGTTCTCGTGCGAGTCACCCGGAATAATATGATT
66 TGCTTCCATACGAGTCACTCTAATCCATCGGGGCTCCCGTGCGAGTCACCCGGAATAATATGATT
36747 AAGTTC
131 AAGTTC
* * *
36753 TCTCGTGCGAGTCTCTCTAATTTATCTGGACTTCCATGTGAGTCACCCGGAATAATATGATTAGG
1 TCTCGTGCGAGTCTCTCTAATTCATCGGGACTTCCATGTGAGTCACCCAGAATAATATGATTAGG
* * *
36818 TGCTTCCATGCGAGTCATTCTAATCCCTCGGGGCTCCCGTGCGAGTCACCCGGAATAATATGATT
66 TGCTTCCATACGAGTCACTCTAATCCATCGGGGCTCCCGTGCGAGTCACCCGGAATAATATGATT
36883 A
131 A
36884 GATGCTTCCG
Statistics
Matches: 116, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
136 116 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.33
Consensus pattern (136 bp):
TCTCGTGCGAGTCTCTCTAATTCATCGGGACTTCCATGTGAGTCACCCAGAATAATATGATTAGG
TGCTTCCATACGAGTCACTCTAATCCATCGGGGCTCCCGTGCGAGTCACCCGGAATAATATGATT
AAGTTC
Found at i:36912 original size:68 final size:68
Alignment explanation
Indices: 36620--36909 Score: 289
Period size: 68 Copynumber: 4.3 Consensus size: 68
36610 TTGTGGTTCT
* * * ** *
36620 CGTGCGAGTCTCTCTAATTCATCGGGACTTCCATGTGAGTCACCTAGAATAATATGATTAGGTGC
1 CGTGCGAGTCACTCTAATTCATCGGGACTCCCATGCGAGTCACCCGGAATAATATGATTAGATGC
36685 TTC
66 TTC
* * * * * * *
36688 TGTACGAGTTACTCTAATTCATTGTGG-TTCTCGTGCGAGTCACCCGGAATAATATGATTA-A-G
1 CGTGCGAGTCACTCTAATTCATCG-GGACTCCCATGCGAGTCACCCGGAATAATATGATTAGATG
*
36750 TTCTC
65 CT-TC
* * * * * *
36755 TCGTGCGAGTCTCTCTAATTTATCTGGACTTCCATGTGAGTCACCCGGAATAATATGATTAGGTG
1 -CGTGCGAGTCACTCTAATTCATCGGGACTCCCATGCGAGTCACCCGGAATAATATGATTAGATG
36820 CTTC
65 CTTC
* * * * * *
36824 CATGCGAGTCATTCTAATCCCTCGGGGCTCCCGTGCGAGTCACCCGGAATAATATGATTAGATGC
1 CGTGCGAGTCACTCTAATTCATCGGGACTCCCATGCGAGTCACCCGGAATAATATGATTAGATGC
36889 TTC
66 TTC
*
36892 CGTGCTAGTCACTCTAAT
1 CGTGCGAGTCACTCTAAT
36910 CCCAACATTG
Statistics
Matches: 173, Mismatches: 43, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
66 2 0.01
67 4 0.02
68 161 0.93
69 4 0.02
70 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (68 bp):
CGTGCGAGTCACTCTAATTCATCGGGACTCCCATGCGAGTCACCCGGAATAATATGATTAGATGC
TTC
Found at i:38312 original size:31 final size:31
Alignment explanation
Indices: 38277--38374 Score: 101
Period size: 31 Copynumber: 3.2 Consensus size: 31
38267 TATTTATGGA
* * *
38277 TTAAATTGATATTTTATCT-AATTTTTAAGAG
1 TTAAATTGATATATTATCTAAAGTTTAAAG-G
38308 TTAAATTGATATATTATCTAAAGTTTAAAGG
1 TTAAATTGATATATTATCTAAAGTTTAAAGG
* * * *
38339 TTAAATTAATATGTTATC-ACAAGTTCAGAGG
1 TTAAATTGATATATTATCTA-AAGTTTAAAGG
38370 TTAAA
1 TTAAA
38375 GTAAAAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.02
31 49 0.84
32 8 0.14
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (31 bp):
TTAAATTGATATATTATCTAAAGTTTAAAGG
Found at i:38644 original size:13 final size:12
Alignment explanation
Indices: 38614--38658 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 12
38604 TGGGTAAGTA
38614 AATAAT-TAAA-
1 AATAATATAAAT
38624 AA-AATATAAAT
1 AATAATATAAAT
38635 AAATAATATAAAT
1 -AATAATATAAAT
38648 AATAA-ATAAAT
1 AATAATATAAAT
38659 TACGTATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
9 3 0.10
10 6 0.19
11 6 0.19
12 7 0.23
13 9 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:40401 original size:40 final size:39
Alignment explanation
Indices: 40347--40425 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 39
40337 CTTTTGACAG
*
40347 TTTTTTTTTGTTTTTGTTTTGGTATATTGATCTTTAGAC
1 TTTTTTTTTGTTTTTGTTTTGGAATATTGATCTTTAGAC
40386 TTTTTATTTTGTTTTTGTTTTGGAATATTGATCTTTAGAC
1 TTTTT-TTTTGTTTTTGTTTTGGAATATTGATCTTTAGAC
40426 AGTTGGCGCC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 5 0.13
40 33 0.87
ACGTcount: A:0.15, C:0.05, G:0.15, T:0.65
Consensus pattern (39 bp):
TTTTTTTTTGTTTTTGTTTTGGAATATTGATCTTTAGAC
Found at i:40577 original size:26 final size:25
Alignment explanation
Indices: 40538--40597 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
40528 TCGATTCGAT
40538 TCGAAAACTGTGAAATGAAACTCAAC
1 TCGAAAACTGTGAAAT-AAACTCAAC
* * *
40564 TCGAAAACTTTGAAATAGACTCGAC
1 TCGAAAACTGTGAAATAAACTCAAC
40589 TCGAAAACT
1 TCGAAAACT
40598 CAAGATACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
25 16 0.52
26 15 0.48
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (25 bp):
TCGAAAACTGTGAAATAAACTCAAC
Found at i:40591 original size:25 final size:26
Alignment explanation
Indices: 40533--40597 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
40523 TAAGCTCGAT
*
40533 TCGATTCGAAAACTGTGAAATGAAAC
1 TCGACTCGAAAACTGTGAAATGAAAC
* * *
40559 TCAACTCGAAAACTTTGAAAT-AGAC
1 TCGACTCGAAAACTGTGAAATGAAAC
40584 TCGACTCGAAAACT
1 TCGACTCGAAAACT
40598 CAAGATACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 16 0.47
26 18 0.53
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (26 bp):
TCGACTCGAAAACTGTGAAATGAAAC
Found at i:41880 original size:60 final size:59
Alignment explanation
Indices: 41751--41880 Score: 136
Period size: 60 Copynumber: 2.2 Consensus size: 59
41741 GAATAGTTAG
* * * *
41751 GTGACCATTTTGTAACTTTTAATAGTTAGATAATTTAACAAAGCAACATCCTATAGTTA
1 GTGACCATTTTGTAACTTTTAATAGTTAGAGAACTCAACAAAGCAACATCCTATAGTCA
* * * * * *
41810 GAAGATCATTTTGTAATTTTTAATAGTTGGAGGACTCAACAAAGTAACA-CCATATAGTCA
1 G-TGACCATTTTGTAACTTTTAATAGTTAGAGAACTCAACAAAGCAACATCC-TATAGTCA
41870 TGTGACCATTT
1 -GTGACCATTT
41881 ATATACTTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
59 3 0.05
60 52 0.93
61 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (59 bp):
GTGACCATTTTGTAACTTTTAATAGTTAGAGAACTCAACAAAGCAACATCCTATAGTCA
Found at i:42390 original size:20 final size:20
Alignment explanation
Indices: 42365--42417 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
42355 CCAACAAATC
42365 CGCAACGCGAATTCCAATTT
1 CGCAACGCGAATTCCAATTT
* * *
42385 CGCAAC-CCAGTTTTCAATTT
1 CGCAACGCGA-ATTCCAATTT
42405 CGCAACGCGAATT
1 CGCAACGCGAATT
42418 TGTAAATCGC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (20 bp):
CGCAACGCGAATTCCAATTT
Found at i:42447 original size:20 final size:19
Alignment explanation
Indices: 42398--42483 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 19
42388 AACCCAGTTT
*
42398 TCAATTTCGCAACGCGAATTTG
1 TCAAATTCGCAACGCGAA---G
*
42420 T-AAA-TCGCAACACAGAAG
1 TCAAATTCGCAACGC-GAAG
42438 TCAAATTCGCAACGCGATAG
1 TCAAATTCGCAACGCGA-AG
42458 TCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAACGCG-AAG
42478 TCAAAT
1 TCAAAT
42484 GTTTTAATGC
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
18 2 0.04
19 5 0.09
20 42 0.75
21 6 0.11
22 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (19 bp):
TCAAATTCGCAACGCGAAG
Found at i:42468 original size:40 final size:40
Alignment explanation
Indices: 42398--42483 Score: 97
Period size: 40 Copynumber: 2.1 Consensus size: 40
42388 AACCCAGTTT
* *
42398 TCAATTTCGCAACGCGAATTTGTAAATCGCAACAC-AGAAG
1 TCAAATTCGCAACGCGAATTAGTAAATCGCAACACGA-AAG
*
42438 TCAAATTCGCAACGCG-A-TAGTCAAATTCGCAACGCGAAAG
1 TCAAATTCGCAACGCGAATTAGT-AAA-TCGCAACACGAAAG
42478 TCAAAT
1 TCAAAT
42484 GTTTTAATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 3 0.08
39 4 0.10
40 32 0.80
41 1 0.03
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (40 bp):
TCAAATTCGCAACGCGAATTAGTAAATCGCAACACGAAAG
Found at i:42631 original size:22 final size:22
Alignment explanation
Indices: 42606--42657 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
42596 ACTCTCTACG
* *
42606 ACGACATCTGTCCCCATCTCCA
1 ACGAAATCTATCCCCATCTCCA
* *
42628 ACGAAATCTATCCCCATTTCCG
1 ACGAAATCTATCCCCATCTCCA
42650 ACGAAATC
1 ACGAAATC
42658 CATCTATCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.38, G:0.10, T:0.23
Consensus pattern (22 bp):
ACGAAATCTATCCCCATCTCCA
Found at i:45175 original size:42 final size:42
Alignment explanation
Indices: 45128--45227 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
45118 GCCCGATGCA
* ** * *
45128 CCTATCATCATTCAAGAGGTGCCTCCTATCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCC
*
45170 CCTATCATCATTGAAGAAGCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCC
* *
45212 CCTGTCATCGTTCAAG
1 CCTATCATCATTCAAG
45228 TGGTCATGCT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATCATTCAAGAAGCCCCTCCCACCGTTCAAGAGGCC
Found at i:45186 original size:21 final size:21
Alignment explanation
Indices: 45128--45227 Score: 76
Period size: 21 Copynumber: 4.8 Consensus size: 21
45118 GCCCGATGCA
**
45128 CCTATCATCATTCAAGAGGTG
1 CCTATCATCATTCAAGAGGCC
* *
45149 CCT-CCTATCGTTCAAGAGGCC
1 CCTATC-ATCATTCAAGAGGCC
* *
45170 CCTATCATCATTGAAGAAGCC
1 CCTATCATCATTCAAGAGGCC
** * *
45191 CCTCCCACCGTTCAAGAGGCC
1 CCTATCATCATTCAAGAGGCC
* *
45212 CCTGTCATCGTTCAAG
1 CCTATCATCATTCAAG
45228 TGGTCATGCT
Statistics
Matches: 60, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 1 0.02
21 58 0.97
22 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.24
Consensus pattern (21 bp):
CCTATCATCATTCAAGAGGCC
Found at i:46623 original size:14 final size:14
Alignment explanation
Indices: 46604--46643 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
46594 TTTTGATTAA
46604 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
46618 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
46632 TTGATTTGTAAA
1 TTGATTTGTAAA
46644 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:46636 original size:61 final size:64
Alignment explanation
Indices: 46553--46693 Score: 175
Period size: 61 Copynumber: 2.2 Consensus size: 64
46543 TTTTACATTG
*
46553 AAAGTTGATTTG-TTACGATTGATGAGGAAATAAGATTTA-TTTTTTG-A-TTAATTGATTTGTA
1 AAAGTTGATTTGTTTAC-ATTGATGAGGAAATAAGAATTATTTTTTTGTATTTAATTGATTTGTA
** *
46614 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTGCTTATTTAATTGATTTG
1 AAAGTTGATTTGTTTACA-TTGATGAGGAAATAAGAATTATTTTTTTG--TATTTAATTGATTTG
46678 TA
63 TA
46680 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
46694 ATTTCTAAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
60 1 0.01
61 29 0.42
62 10 0.14
65 1 0.01
66 28 0.41
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.50
Consensus pattern (64 bp):
AAAGTTGATTTGTTTACATTGATGAGGAAATAAGAATTATTTTTTTGTATTTAATTGATTTGTA
Found at i:47026 original size:39 final size:39
Alignment explanation
Indices: 46972--47058 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
46962 TCAAGTTGTA
46972 GATTTTGATTTCCTTTTCCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTCCTTGGCACCATATGAGATTTG
* *
47011 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTCCTTGGCACCATATGAGATTTG
47050 GATTTTGAT
1 GATTTTGAT
47059 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTCCTTGGCACCATATGAGATTTG
Found at i:47383 original size:18 final size:18
Alignment explanation
Indices: 47360--47396 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47350 GCCGAAATTT
47360 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
47378 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
47396 A
1 A
47397 CTCCAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:47813 original size:25 final size:25
Alignment explanation
Indices: 47779--47828 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
47769 ATTATTTTTC
*
47779 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
47804 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
47829 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:50387 original size:3 final size:3
Alignment explanation
Indices: 50379--50412 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
50369 TCTTCGGGGA
*
50379 CTT CTT CTT CTT CTT CTT CTT CTT TTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
50413 AGGGTTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:50621 original size:24 final size:24
Alignment explanation
Indices: 50587--50640 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
50577 CCATCACATC
50587 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
50611 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
50635 ATCAAA
1 ATCAAA
50641 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:50654 original size:24 final size:24
Alignment explanation
Indices: 50587--50654 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
50577 CCATCACATC
* * *
50587 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
50611 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
50635 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
50655 TAGTACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:50787 original size:12 final size:12
Alignment explanation
Indices: 50766--50799 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
50756 GGTTGTGGGT
*
50766 TTTGAGATTGTG
1 TTTGATATTGTG
50778 TTTGATATTGTG
1 TTTGATATTGTG
*
50790 TTTGGTATTG
1 TTTGATATTG
50800 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:51571 original size:19 final size:19
Alignment explanation
Indices: 51544--51693 Score: 97
Period size: 20 Copynumber: 7.6 Consensus size: 19
51534 ACTAAAACCT
51544 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
51563 GTTGTGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
**
51582 GTTGCGAATTTGACTTTC-
1 GTTGCGAATTTGAAATTCA
**
51600 GCATTGCGAATTTGACTTTC-
1 G--TTGCGAATTTGAAATTCA
** *
51620 GCATTGCGAATTTGACTTTCGC
1 G--TTGCGAATTTGAAATTC-A
** *
51642 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTC-A
** *
51662 GTTGCGAATTTGACTTTCGT
1 GTTGCGAATTTGAAATTC-A
51682 GTTGCGAATTTG
1 GTTGCGAATTTG
51694 GAATATCGCA
Statistics
Matches: 122, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
18 1 0.01
19 33 0.27
20 87 0.71
22 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:51608 original size:20 final size:20
Alignment explanation
Indices: 51582--51693 Score: 197
Period size: 20 Copynumber: 5.6 Consensus size: 20
51572 TTGAAATTCA
51582 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCGC
*
51602 ATTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCGC
*
51622 ATTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCGC
51642 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTCGC
*
51662 GTTGCGAATTTGACTTTCGT
1 GTTGCGAATTTGACTTTCGC
51682 GTTGCGAATTTG
1 GTTGCGAATTTG
51694 GAATATCGCA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 89 1.00
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCGC
Found at i:51711 original size:21 final size:21
Alignment explanation
Indices: 51685--51730 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
51675 CTTTCGTGTT
* *
51685 GCGAATTTGGAATATCGCAAC
1 GCGAATTTGAAAAATCGCAAC
*
51706 GCGAATTTGAAAAATCGCAAT
1 GCGAATTTGAAAAATCGCAAC
51727 GCGA
1 GCGA
51731 TTTACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (21 bp):
GCGAATTTGAAAAATCGCAAC
Found at i:51787 original size:20 final size:20
Alignment explanation
Indices: 51738--51791 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
51728 CGATTTACAT
51738 ATTCGTGTTGCGAAATTGGA
1 ATTCGTGTTGCGAAATTGGA
*
51758 A-ACTGTGTTGCGAAATTGGA
1 ATTC-GTGTTGCGAAATTGGA
*
51778 ATTCGCGTTGCGAA
1 ATTCGTGTTGCGAA
51792 TTTGTTGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.31
Consensus pattern (20 bp):
ATTCGTGTTGCGAAATTGGA
Found at i:55851 original size:33 final size:33
Alignment explanation
Indices: 55813--55877 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
55803 AAATATTATC
55813 CAAAAGTTTGACTGTAAG-GACGATCTAGATGTT
1 CAAAAGTTTGACTGTAAGTGAC-ATCTAGATGTT
*
55846 CAAAAGTTTGACTGTAAGTGACATGTAGATGT
1 CAAAAGTTTGACTGTAAGTGACATCTAGATGT
55878 CGGATAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.31
Consensus pattern (33 bp):
CAAAAGTTTGACTGTAAGTGACATCTAGATGTT
Found at i:57129 original size:21 final size:20
Alignment explanation
Indices: 57089--57151 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 20
57079 ATTTAAGGAA
*
57089 TATAAAAATCTGAAAATATT
1 TATAAAAATATGAAAATATT
*
57109 TATAAAACATATGAAATTATT
1 TATAAAA-ATATGAAAATATT
57130 TATTAAAAATATGAAAATATT
1 TA-TAAAAATATGAAAATATT
57151 T
1 T
57152 TATTTATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.18
21 26 0.68
22 5 0.13
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
TATAAAAATATGAAAATATT
Found at i:57913 original size:24 final size:24
Alignment explanation
Indices: 57897--57982 Score: 154
Period size: 24 Copynumber: 3.6 Consensus size: 24
57887 GTTCGTGAAC
*
57897 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
57921 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
*
57945 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
57969 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
57983 ATTCATTTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.09, C:0.13, G:0.24, T:0.53
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:57915 original size:14 final size:14
Alignment explanation
Indices: 57896--57975 Score: 95
Period size: 14 Copynumber: 6.3 Consensus size: 14
57886 CGTTCGTGAA
57896 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
57910 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
57924 CG-T---TTATGTT
1 CGTTCGGTTATGTT
57934 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
57948 CG-T---TTATGTT
1 CGTTCGGTTATGTT
*
57958 CGTTCGATTATGTT
1 CGTTCGGTTATGTT
57972 CGTT
1 CGTT
57976 TATGTTCATT
Statistics
Matches: 58, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
10 18 0.31
11 2 0.03
13 2 0.03
14 36 0.62
ACGTcount: A:0.09, C:0.14, G:0.25, T:0.53
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:57992 original size:24 final size:24
Alignment explanation
Indices: 57897--57995 Score: 137
Period size: 24 Copynumber: 4.1 Consensus size: 24
57887 GTTCGTGAAC
* *
57897 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCAGTTAT
*
57921 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCAGTTAT
57945 GTTCGTTTATGTTCGTTC-GATTAT
1 GTTCGTTTATGTTCGTTCAG-TTAT
* *
57969 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCGTTCAGTTAT
57993 GTT
1 GTT
57996 TAACCCAATC
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
23 1 0.01
24 69 0.99
ACGTcount: A:0.11, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCAGTTAT
Found at i:57993 original size:48 final size:48
Alignment explanation
Indices: 57897--57995 Score: 153
Period size: 48 Copynumber: 2.1 Consensus size: 48
57887 GTTCGTGAAC
* * *
57897 GTTCGGTTATGTTCGTTCGGTTATGTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCGTTCGATTATGTTCGTTTATGTTCATTCAGTTAT
* *
57945 GTTCGTTTATGTTCGTTCGATTATGTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCGTTCGATTATGTTCGTTTATGTTCATTCAGTTAT
57993 GTT
1 GTT
57996 TAACCCAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.11, C:0.12, G:0.22, T:0.55
Consensus pattern (48 bp):
GTTCGGTTATGTTCGTTCGATTATGTTCGTTTATGTTCATTCAGTTAT
Found at i:58738 original size:10 final size:10
Alignment explanation
Indices: 58723--58797 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
58713 GGGTCTCCAA
58723 CGTTTATGTT
1 CGTTTATGTT
58733 CGTTTATGTT
1 CGTTTATGTT
58743 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
58754 ATGTTCGTGTT
1 -CGTTTATGTT
58765 CGTTTATGTT
1 CGTTTATGTT
58775 CG----TGTT
1 CGTTTATGTT
58781 CGTTTATGTT
1 CGTTTATGTT
58791 CGTTTAT
1 CGTTTAT
58798 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:58754 original size:16 final size:16
Alignment explanation
Indices: 58729--58793 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
58719 CCAACGTTTA
58729 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
58745 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
58761 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
58777 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
58793 T
1 T
58794 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:58883 original size:16 final size:16
Alignment explanation
Indices: 58862--58894 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
58852 AAAAAAAATT
58862 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
58878 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
58894 T
1 T
58895 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:60311 original size:5 final size:6
Alignment explanation
Indices: 60294--60318 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
60284 ATTATAATTA
60294 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
60319 GTTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:60317 original size:17 final size:18
Alignment explanation
Indices: 60275--60332 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
60265 TTATGTAAAA
60275 TATATTTTTATTATAA-T
1 TATATTTTTATTATAATT
* *
60292 TATATTTTTATTTTTATT
1 TATATTTTTATTATAATT
* *
60310 TTTATTTTTGTT-TAAATT
1 TATATTTTTATTAT-AATT
60328 TATAT
1 TATAT
60333 AATTAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 15 0.45
18 18 0.55
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TATATTTTTATTATAATT
Found at i:66705 original size:21 final size:21
Alignment explanation
Indices: 66681--66742 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
66671 CAAACTTTAC
*
66681 CAAACTTTGAAAAATATTTTT
1 CAAACTTTGAAAAACATTTTT
**
66702 CAAA-----AAAAACATTTAC
1 CAAACTTTGAAAAACATTTTT
66718 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
66739 CAAA
1 CAAA
66743 GTTGGTTGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
16 13 0.42
21 18 0.58
ACGTcount: A:0.50, C:0.15, G:0.03, T:0.32
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:66726 original size:37 final size:36
Alignment explanation
Indices: 66672--66742 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 36
66662 AACATCTACC
*
66672 AAACTTTACCAAACTTTGAAAAATATTTTTCAAAAA
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAAA
66708 AAACATTTACCAAACTTTGAAAAACATTTTTCAAA
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAA
66743 GTTGGTTGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.32
Consensus pattern (36 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAAA
Found at i:71252 original size:21 final size:21
Alignment explanation
Indices: 71228--71288 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
71218 AAACATCTAA
71228 CAAACTTTAAAAAACATTTTT
1 CAAACTTTAAAAAACATTTTT
**
71249 C--A----AAAAAACATTTAC
1 CAAACTTTAAAAAACATTTTT
*
71264 CAAACTTTGAAAAACATTTTT
1 CAAACTTTAAAAAACATTTTT
71285 CAAA
1 CAAA
71289 GTTGGTTGTC
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 12 0.41
17 1 0.03
19 1 0.03
21 15 0.52
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (21 bp):
CAAACTTTAAAAAACATTTTT
Found at i:71268 original size:36 final size:36
Alignment explanation
Indices: 71210--71288 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
71200 CTCATTCCTA
*
71210 TTTTC-AACAAACATCTAACAAACTTTAAAAAACAT
1 TTTTCAAAAAAACATCTAACAAACTTTAAAAAACAT
* * *
71245 TTTTCAAAAAAACATTTACCAAACTTTGAAAAACAT
1 TTTTCAAAAAAACATCTAACAAACTTTAAAAAACAT
71281 TTTTCAAA
1 TTTTCAAA
71289 GTTGGTTGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 5 0.13
36 34 0.87
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (36 bp):
TTTTCAAAAAAACATCTAACAAACTTTAAAAAACAT
Found at i:78986 original size:175 final size:176
Alignment explanation
Indices: 78694--79014 Score: 511
Period size: 175 Copynumber: 1.8 Consensus size: 176
78684 TCACATCTAC
78694 CCATTGGTTTAGTTATCATTGATTCACATGAAAAAATTGCTTTGCTAAGACCAAATATATGATTC
1 CCATTGGTTTAGTTATCATTGATTCACATGAAAAAATTGCTTTGCTAAGACCAAATATATGATTC
* * * *
78759 ACATGAAAATTCTTTCTAGAGTTATTACATCGATTGTGATGACCTGCAAATGCCAACACCTGCAT
66 ACATGAAAATTCTTTCCAAAGGTATTACATCGATTGTGATGACCTGCAAATGCCAACACCTACAT
*
78824 GCACTATGATTCATATGTTTTCCATTTCGGCATTGTAGAAGTTTTG
131 GCACTAAGATTCATATGTTTTCCATTTCGGCATTGTAGAAGTTTTG
* * * *
78870 CCATTGGTTATAGTTATCCTTGA-TCACATG-AAAAATTGTTTTGCTAAGAGCAGATATATGATT
1 CCATTGGTT-TAGTTATCATTGATTCACATGAAAAAATTGCTTTGCTAAGACCAAATATATGATT
* * *
78933 CACATGAAAATTCTTTCCAAAGGTATTAGATTGATTGTGATGACCTGCAAATGCCGACACCTACA
65 CACATGAAAATTCTTTCCAAAGGTATTACATCGATTGTGATGACCTGCAAATGCCAACACCTACA
78998 TGCACTAAGATTCATAT
130 TGCACTAAGATTCATAT
79015 ACTCGGCACT
Statistics
Matches: 132, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
175 104 0.79
176 16 0.12
177 12 0.09
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (176 bp):
CCATTGGTTTAGTTATCATTGATTCACATGAAAAAATTGCTTTGCTAAGACCAAATATATGATTC
ACATGAAAATTCTTTCCAAAGGTATTACATCGATTGTGATGACCTGCAAATGCCAACACCTACAT
GCACTAAGATTCATATGTTTTCCATTTCGGCATTGTAGAAGTTTTG
Found at i:83122 original size:66 final size:65
Alignment explanation
Indices: 82933--83504 Score: 306
Period size: 66 Copynumber: 8.7 Consensus size: 65
82923 GGTCGTTATT
* * * * * *
82933 GTCGGGTTCGAGTTTATTCAAGTTCAGCTCAACCTGAAATATGGATAATATTTT-T-TATTCATT
1 GTCGGGTTCGAGTTTATTTAGGTTCAG-TTAACTTGAAATATGGGTAACATTTTATCTATTCATT
82996 G
65 G
* * * * * * * *
82997 TTCAGGTTGGAGTTTATTTAGGTTCAACTTTACTTG-AATATAGGCAACATTTTATCTATTCGTT
1 GTCGGGTTCGAGTTTATTTAGGTTC-AGTTAACTTGAAATATGGGTAACATTTTATCTATTCATT
83061 G
65 G
* * **
83062 GTCGGGTTCGAGTTTATTTAGGTTTAGATTAATTTGAAATATGGGTAACATTTTATCTATTTGTT
1 GTCGGGTTCGAGTTTATTTAGGTTCAG-TTAACTTGAAATATGGGTAACATTTTATCTATTCATT
83127 G
65 G
* * ** * *
83128 ATTGTATTTGAGTTTATTTAGG-T---TTAACTTGAAATATGGGTAACATTTTATCTATTCATTA
1 GTCGGGTTCGAGTTTATTTAGGTTCAGTTAACTTGAAATATGGGTAACATTTTATCTATTCATTG
* * * * * * *
83189 GTCAGGTTCAAGTTTATTCT-GGTTTAGCTCAACCTGAAATATGGGTAACATTTTGTATATTCAT
1 GTCGGGTTCGAGTTTATT-TAGGTTCAG-TTAACTTGAAATATGGGTAACATTTTATCTATTCAT
83253 TG
64 TG
** * *
83255 GTCGGGCTT-GAG-TTATGCAGGTTCAGTTCAATTTGAAA-AGTAGGTAACATTTTATGTATTCA
1 GTCGGG-TTCGAGTTTATTTAGGTTCAGTT-AACTTGAAATA-TGGGTAACA--TT-T-TA-TC-
*
83317 TTAGTCTCGTTG
57 -TA-T-TCATTG
* * * * * * * * *
83329 GTCGGATTTGAGTTTATTCAGGTTCAACTCAATTTGAAATATGGGAAACATTTTATATA-TGAGT
1 GTCGGGTTCGAGTTTATTTAGGTTC-AGTTAACTTGAAATATGGGTAACATTTTATCTATTCA-T
83393 TG
64 TG
* * ** * * * * * * *
83395 ATCGAGTTTAAGTTTATTCAAGTTGAATTCAACTTGAAATATGAGTGACATTTTATTTATTCATT
1 GTCGGGTTCGAGTTTATTTAGGTTCAGTT-AACTTGAAATATGGGTAACATTTTATCTATTCATT
83460 G
65 G
* * * * *
83461 ATTGGATCCGAGTTTATTCTA-GTTCAGTTCAACTTGAAGTATGG
1 GTCGGGTTCGAGTTTATT-TAGGTTCAGTT-AACTTGAAATATGG
83505 ATAATATTGG
Statistics
Matches: 385, Mismatches: 91, Indels: 62
0.72 0.17 0.12
Matches are distributed among these distances:
61 47 0.12
62 2 0.01
63 13 0.03
64 29 0.08
65 65 0.17
66 163 0.42
67 7 0.02
68 3 0.01
69 1 0.00
70 2 0.01
71 2 0.01
72 3 0.01
73 5 0.01
74 13 0.03
75 27 0.07
76 3 0.01
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.43
Consensus pattern (65 bp):
GTCGGGTTCGAGTTTATTTAGGTTCAGTTAACTTGAAATATGGGTAACATTTTATCTATTCATTG
Found at i:83266 original size:127 final size:125
Alignment explanation
Indices: 82937--83268 Score: 326
Period size: 127 Copynumber: 2.6 Consensus size: 125
82927 GTTATTGTCG
** * * * * *
82937 GGTTCGAGTTTATTCAAGTTCAGCTCAACCTGAAATATGGATAATATTTTTTATTCATTGTTCAG
1 GGTTCGAGTTTATTCTGGTTTAGCTCAACCTGAAATATGGGTAACATTTTTTATTCATTGATCGG
* * * *
83002 GTTGGAGTTTATTTAGGTTCAACTTTACTTGAATATAGGCAACATTTTATCTATTCGTTGGTCG
66 GTT-GAGTTTATTTAGGTTCAACTTGA--T-AATATAGGCAACATTTTATCTATTCATTAGTCA
* * ** **
83066 GGTTCGAGTTTATT-TAGGTTTAGATTAATTTGAAATATGGGTAACATTTTATCTATTTGTTGAT
1 GGTTCGAGTTTATTCT-GGTTTAGCTCAACCTGAAATATGGGTAACATTTT-T-TATTCATTGAT
* ** * * *
83130 TGTATTTGAGTTTATTTAGGTTTAACTTGA-AATATGGGTAACATTTTATCTATTCATTAGTCA
63 CG-GGTTGAGTTTATTTAGGTTCAACTTGATAATATAGGCAACATTTTATCTATTCATTAGTCA
* *
83193 GGTTCAAGTTTATTCTGGTTTAGCTCAACCTGAAATATGGGTAACATTTTGTATATTCATTGGTC
1 GGTTCGAGTTTATTCTGGTTTAGCTCAACCTGAAATATGGGTAACATTTT-T-TATTCATTGATC
83258 GGGCTTGAGTT
64 GGG-TTGAGTT
83269 ATGCAGGTTC
Statistics
Matches: 161, Mismatches: 36, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
127 88 0.55
128 1 0.01
129 40 0.25
130 1 0.01
131 29 0.18
132 2 0.01
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.44
Consensus pattern (125 bp):
GGTTCGAGTTTATTCTGGTTTAGCTCAACCTGAAATATGGGTAACATTTTTTATTCATTGATCGG
GTTGAGTTTATTTAGGTTCAACTTGATAATATAGGCAACATTTTATCTATTCATTAGTCA
Found at i:86259 original size:20 final size:20
Alignment explanation
Indices: 86222--86265 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
86212 ATTCAAGCAG
* * *
86222 AGAAGGAAAAAAGGAAAGGA
1 AGAAAGAAAAAAAGAAAGAA
*
86242 AGAAAGAAAAAAATAAAGAA
1 AGAAAGAAAAAAAGAAAGAA
86262 AGAA
1 AGAA
86266 GAGGTAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAAAAAGAAAGAA
Found at i:88994 original size:37 final size:37
Alignment explanation
Indices: 88935--89005 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
88925 TTTATTGTCG
*
88935 TGCTACCTTTCGATCACTCTTCCTCTCCCAAATGTAT
1 TGCTACCTCTCGATCACTCTTCCTCTCCCAAATGTAT
*
88972 TGCTGCCTCTCGATCACTCTTCCTCTCCCAAATG
1 TGCTACCTCTCGATCACTCTTCCTCTCCCAAATG
89006 CTCTACTGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.17, C:0.38, G:0.10, T:0.35
Consensus pattern (37 bp):
TGCTACCTCTCGATCACTCTTCCTCTCCCAAATGTAT
Found at i:89015 original size:37 final size:37
Alignment explanation
Indices: 88944--89016 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
88934 GTGCTACCTT
* *
88944 TCGATCACTCTTCCTCTCCCAAATGTATTGCTGCCTC
1 TCGATCACTCTTCCTCTCCCAAATGTACTACTGCCTC
88981 TCGATCACTCTTCCTCTCCCAAATGCT-CTACTGCCT
1 TCGATCACTCTTCCTCTCCCAAATG-TACTACTGCCT
89017 AATCTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 32 0.97
38 1 0.03
ACGTcount: A:0.16, C:0.40, G:0.10, T:0.34
Consensus pattern (37 bp):
TCGATCACTCTTCCTCTCCCAAATGTACTACTGCCTC
Found at i:92259 original size:10 final size:9
Alignment explanation
Indices: 92231--92258 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
92221 CATATAGTGG
92231 TATTTTTTT
1 TATTTTTTT
92240 TATTTTTTT
1 TATTTTTTT
92249 TATTTTTTT
1 TATTTTTTT
92258 T
1 T
92259 TGTGGGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TATTTTTTT
Found at i:93154 original size:32 final size:32
Alignment explanation
Indices: 93118--93184 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
93108 ATATGTCATG
* *
93118 TCACTTAAAATAATCACATGATATGTGTTTCA
1 TCACTTAAAATAATCACACGATATGTGTTACA
* * *
93150 TCACTTAAAGTAATGATACGATATGTGTTACA
1 TCACTTAAAATAATCACACGATATGTGTTACA
93182 TCA
1 TCA
93185 ATAATTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (32 bp):
TCACTTAAAATAATCACACGATATGTGTTACA
Found at i:98066 original size:15 final size:16
Alignment explanation
Indices: 98046--98079 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
98036 GAAAACCTTT
98046 AAAGAAAAA-TAAAAG
1 AAAGAAAAAGTAAAAG
98061 AAAGAAAAAGTAAAAG
1 AAAGAAAAAGTAAAAG
98077 AAA
1 AAA
98080 AAGTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAGTAAAAG
Found at i:98078 original size:12 final size:12
Alignment explanation
Indices: 98061--98087 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
98051 AAAATAAAAG
98061 AAAGAAAAAGTA
1 AAAGAAAAAGTA
98073 AAAGAAAAAGTA
1 AAAGAAAAAGTA
98085 AAA
1 AAA
98088 TTTTATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (12 bp):
AAAGAAAAAGTA
Found at i:101840 original size:21 final size:21
Alignment explanation
Indices: 101807--101846 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
101797 TCTCTTAAAA
*
101807 CTATCGAATCTAAAAACAAAG
1 CTATCGAACCTAAAAACAAAG
*
101828 CTATTGAACCTAAAAACAA
1 CTATCGAACCTAAAAACAA
101847 GTGTAGTATG
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:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (21 bp):
CTATCGAACCTAAAAACAAAG
Found at i:106706 original size:13 final size:13
Alignment explanation
Indices: 106688--106713 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
106678 GTATGAATCT
106688 GGAACTTTTCCTG
1 GGAACTTTTCCTG
106701 GGAACTTTTCCTG
1 GGAACTTTTCCTG
106714 CTTGTCTAAG
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:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
GGAACTTTTCCTG
Found at i:112058 original size:3 final size:3
Alignment explanation
Indices: 112052--112081 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
112042 CTTCTTTTAT
112052 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
112082 ATTTACAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:114190 original size:26 final size:26
Alignment explanation
Indices: 114161--114225 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
114151 GTCATAAATC
114161 TATGACGCGCATTTATGACACGCATT
1 TATGACGCGCATTTATGACACGCATT
* *
114187 TATGACACACATTTATGACACGCATT
1 TATGACGCGCATTTATGACACGCATT
*
114213 TATGATGCGCATT
1 TATGACGCGCATT
114226 GAACGTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (26 bp):
TATGACGCGCATTTATGACACGCATT
Found at i:114225 original size:13 final size:13
Alignment explanation
Indices: 114161--114217 Score: 96
Period size: 13 Copynumber: 4.4 Consensus size: 13
114151 GTCATAAATC
*
114161 TATGACGCGCATT
1 TATGACACGCATT
114174 TATGACACGCATT
1 TATGACACGCATT
*
114187 TATGACACACATT
1 TATGACACGCATT
114200 TATGACACGCATT
1 TATGACACGCATT
114213 TATGA
1 TATGA
114218 TGCGCATTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:114302 original size:85 final size:85
Alignment explanation
Indices: 114201--114358 Score: 228
Period size: 85 Copynumber: 1.9 Consensus size: 85
114191 ACACACATTT
*
114201 ATGACACGCATTTATGA-TGCGCATTGAACGTCATTGAAGCCCCCGTCATAAATAAAGATGACAC
1 ATGACACGCATTTATGACT-CACATTGAACGTCATTGAAGCCCCCGTCATAAATAAAGATGACAC
114265 ACATTTGTGTGTCATAAATTA
65 ACATTTGTGTGTCATAAATTA
* * * *** *
114286 ATGACATGTATTTATGACTTACATTGCGTGTCATTGAAGCCCCCGTCATAAATGAAGATGACACA
1 ATGACACGCATTTATGACTCACATTGAACGTCATTGAAGCCCCCGTCATAAATAAAGATGACACA
114351 CATTTGTG
66 CATTTGTG
114359 GGAATTTATC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 63 0.98
86 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (85 bp):
ATGACACGCATTTATGACTCACATTGAACGTCATTGAAGCCCCCGTCATAAATAAAGATGACACA
CATTTGTGTGTCATAAATTA
Found at i:118406 original size:18 final size:17
Alignment explanation
Indices: 118376--118432 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 17
118366 ATTATTATAT
118376 ATATTATTTTAATAATTA
1 ATATT-TTTTAATAATTA
*
118394 ATATTTTTGTAATGATTAA
1 ATATTTTT-TAATAATT-A
118413 TATATTATTTTAATAATTA
1 -ATATT-TTTTAATAATTA
118432 A
1 A
118433 CAGTTAGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 3 0.09
18 13 0.39
19 2 0.06
20 12 0.36
21 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
ATATTTTTTAATAATTA
Found at i:118426 original size:20 final size:20
Alignment explanation
Indices: 118369--118432 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
118359 ATAATTCATT
118369 ATTATATATATTATTTTAATA
1 ATTA-ATATATTATTTTAATA
* *
118390 ATTAATAT-TT-TTGTAATG
1 ATTAATATATTATTTTAATA
118408 ATTAATATATTATTTTAATA
1 ATTAATATATTATTTTAATA
118428 ATTAA
1 ATTAA
118433 CAGTTAGGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 14 0.38
19 4 0.11
20 15 0.41
21 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTAATATATTATTTTAATA
Found at i:118444 original size:38 final size:39
Alignment explanation
Indices: 118369--118444 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 39
118359 ATAATTCATT
* * **
118369 ATTATATATATTATTTTAATAATTAATATTTTTGTAATG
1 ATTATATATATTATTTTAATAATTAACAGTTAGGTAATG
118408 ATTA-ATATATTATTTTAATAATTAACAGTTAGGTAAT
1 ATTATATATATTATTTTAATAATTAACAGTTAGGTAAT
118445 CTCCTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 29 0.88
39 4 0.12
ACGTcount: A:0.41, C:0.01, G:0.07, T:0.51
Consensus pattern (39 bp):
ATTATATATATTATTTTAATAATTAACAGTTAGGTAATG
Done.