Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008145.1 Hibiscus syriacus cultivar Beakdansim tig00110709_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: 110128
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:8502 original size:3 final size:3
Alignment explanation
Indices: 8494--8535 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
8484 CAAAAATGAT
8494 TAA TAA TAA TAA TAA -ACA TAA TAA TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA T-AA TAA TAA TA
8536 GTTTAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 1 0.03
3 31 0.86
4 4 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:8517 original size:18 final size:16
Alignment explanation
Indices: 8495--8535 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
8485 AAAAATGATT
8495 AATAATAATAATAA-A
1 AATAATAATAATAATA
*
8510 CATAATAATAATAATA
1 AATAATAATAATAATA
8526 AATAATAATA
1 AATAATAATA
8536 GTTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:8792 original size:40 final size:40
Alignment explanation
Indices: 8686--8800 Score: 110
Period size: 40 Copynumber: 2.8 Consensus size: 40
8676 TGTTGGTTTT
8686 GGGATGACACTGCTCATACGTGATGAAGAGTTCGGTCGTCTAA
1 GGGATGACACTGCTCATACGTGATGAAGAGTTCGGTCG--T-A
* * * * * *
8729 GGG-TGACACGGATCCTACATGATGAGGA-TATCTGGTCG-G
1 GGGATGACACTGCTCATACGTGATGAAGAGT-TC-GGTCGTA
8768 GGGATGACACTGCTCATACGTGATGAAGAGTTC
1 GGGATGACACTGCTCATACGTGATGAAGAGTTC
8801 TTGGTCATCT
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
39 3 0.05
40 22 0.39
41 2 0.04
42 22 0.39
43 8 0.14
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.24
Consensus pattern (40 bp):
GGGATGACACTGCTCATACGTGATGAAGAGTTCGGTCGTA
Found at i:9057 original size:134 final size:135
Alignment explanation
Indices: 8729--9178 Score: 542
Period size: 134 Copynumber: 3.4 Consensus size: 135
8719 GGTCGTCTAA
* ** * **
8729 GGGTGACACGGA-TCCTACATGATGAGGATATCTGGTCGGGGGATGACACTGCTCATACGTGATG
1 GGGTGACAC-GACTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACAACTCATACGTGATG
* * * * *
8793 AAGAGTTCTTGGTCATCTTTAGGA-AGGGTGATAACTCAGTTCCTACGCGATGAAGACTGCTGGT
65 AAGAGTTC-TGGCCATCTTTAGGAGAGGGTGATAACACGGTTCCTACGTGATGAGGAC-GCTGGT
8857 TATCTAT-
128 TATCTATG
* * * * *
8864 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATAACATAGCTCATACGTGATGA
1 GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACAACTCATACGTGATGA
8929 AGAGTTCTGGCCATCTTTAGGAGA-GGTGATAACACGGTTCCTACGTGATGAGGACAGCTGGTTA
66 AGAGTTCTGGCCATCTTTAGGAGAGGGTGATAACACGGTTCCTACGTGATGAGGAC-GCTGGTTA
8993 TCTATG
130 TCTATG
* * * * * *
8999 GGGTGACATGACTCCTACGTGATGAGGAGGTCTAGT-AAGGGATGACACAATTCCTACGTGAAGA
1 GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACAACTCATACGTGATGA
* * * *
9063 GGA-TGGCTGACCATCTTTAGG-GAGGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTT
66 AGAGT-TCTGGCCATCTTTAGGAGAGGGTGATAACACGGTTCCTACGTGATGAGGACG-CTGGTT
9126 ATC--TG
129 ATCTATG
9131 GGGTGACACGACTCCTACGTGATGAGGA-GTCTGGTCAGGGGATGACAC
1 GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACAC
9179 GTTCCTATAT
Statistics
Matches: 277, Mismatches: 31, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
131 6 0.02
132 40 0.14
133 4 0.01
134 130 0.47
135 97 0.35
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (135 bp):
GGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCAGGGGATGACACAACTCATACGTGATGA
AGAGTTCTGGCCATCTTTAGGAGAGGGTGATAACACGGTTCCTACGTGATGAGGACGCTGGTTAT
CTATG
Found at i:9319 original size:28 final size:30
Alignment explanation
Indices: 9287--9343 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
9277 CTCAAAGATA
*
9287 ATGG-TGTTTCAAAAGAAA-CGACTCAAAG
1 ATGGTTGTTTCAAAAGAAATAGACTCAAAG
*
9315 ATGGTTTGTTTCAAGAGAAATAGACTCAA
1 ATGG-TTGTTTCAAAAGAAATAGACTCAA
9344 TGATTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
30 13 0.54
31 7 0.29
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (30 bp):
ATGGTTGTTTCAAAAGAAATAGACTCAAAG
Found at i:9327 original size:30 final size:30
Alignment explanation
Indices: 9291--9366 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
9281 AAGATAATGG
9291 TGTTTCAAAAGAAACGACTCAAAGATGGTT-
1 TGTTTCAAAAGAAACGACTCAAAGAT-GTTA
* * * *
9321 TGTTTCAAGAGAAATAGACTCAATGATTTTA
1 TGTTTCAAAAGAAA-CGACTCAAAGATGTTA
*
9352 TGTTTCCAAAGAAAC
1 TGTTTCAAAAGAAAC
9367 TGCCTCAAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 15 0.41
31 22 0.59
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.30
Consensus pattern (30 bp):
TGTTTCAAAAGAAACGACTCAAAGATGTTA
Found at i:10160 original size:38 final size:36
Alignment explanation
Indices: 10118--10190 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
10108 AAACAAATTT
*
10118 AAATTTGTATCTCAGAGAAAAATGTCTCAAGCGAGACG
1 AAATTTGT-TCTCAGA-AAAAATATCTCAAGCGAGACG
* * *
10156 AAATTTGTTTTTAGAAAAATTATCTCAAGCGAGAC
1 AAATTTGTTCTCAGAAAAAATATCTCAAGCGAGAC
10191 AAAGGTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 18 0.58
37 5 0.16
38 8 0.26
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (36 bp):
AAATTTGTTCTCAGAAAAAATATCTCAAGCGAGACG
Found at i:10203 original size:36 final size:36
Alignment explanation
Indices: 10133--10220 Score: 101
Period size: 36 Copynumber: 2.4 Consensus size: 36
10123 TGTATCTCAG
*
10133 AGAAAAATGTCTCAAGCGAGACGAAA-TT-TGTTTTT
1 AGAAAAATATCTCAAGCGAGACGAAAGTTAT-TTTTT
10168 AGAAAAATTATCTCAAGCGAGAC-AAAGGTTATTTTTT
1 AGAAAAA-TATCTCAAGCGAGACGAAA-GTTATTTTTT
**
10205 AGAAAACGATCTCAAG
1 AGAAAAATATCTCAAG
10221 TGAAATCAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
35 10 0.22
36 22 0.48
37 13 0.28
38 1 0.02
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.28
Consensus pattern (36 bp):
AGAAAAATATCTCAAGCGAGACGAAAGTTATTTTTT
Found at i:10331 original size:36 final size:36
Alignment explanation
Indices: 10254--10348 Score: 102
Period size: 36 Copynumber: 2.5 Consensus size: 36
10244 AAGAAAATTC
* * *
10254 AAAATTTGTATCTCAAAGGGAAAATGTCTCAAGTGAGAC-
1 AAAATTTGT-T-TCAAA-GG-AACTGTCTCAAATGAAACA
*
10293 AAAATTTGTTTTCGAAGGAACTGTCTCAAATGAAACA
1 AAAATTTG-TTTCAAAGGAACTGTCTCAAATGAAACA
10330 AAAATTTGTTTCAAAGGAA
1 AAAATTTGTTTCAAAGGAA
10349 ACAAACACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
36 25 0.51
37 10 0.20
38 4 0.08
39 9 0.18
40 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (36 bp):
AAAATTTGTTTCAAAGGAACTGTCTCAAATGAAACA
Found at i:10703 original size:4 final size:4
Alignment explanation
Indices: 10694--11704 Score: 1812
Period size: 4 Copynumber: 255.8 Consensus size: 4
10684 ATGCAAAATT
*
10694 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
10740 TATG TATG TATG TATA TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
10788 TATG TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10836 TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10882 TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10928 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
10976 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11024 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11072 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11120 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11168 TATG TATG TATG TATG TATG TATG TATG TATG CATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
11216 TATG TATG TATG TATG TATG TATT TATG TATT TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11264 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11312 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
11360 TATA TATG TATC TATG TATC TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11408 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11456 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11504 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
11552 TATG TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11600 TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
11646 TATG TATG TA-- TATA TATG TATG TTTG TATA TATG --TG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
11690 TATG TATG TATG TAT
1 TATG TATG TATG TAT
11705 ATTTTCTCGA
Statistics
Matches: 969, Mismatches: 26, Indels: 24
0.95 0.03 0.02
Matches are distributed among these distances:
2 12 0.01
4 957 0.99
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:13046 original size:15 final size:16
Alignment explanation
Indices: 13026--13059 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13016 ATTGTTTTTG
13026 TTTTTGCT-TTTCTTT
1 TTTTTGCTCTTTCTTT
*
13041 TTTTTGCTCTTTGTTT
1 TTTTTGCTCTTTCTTT
13057 TTT
1 TTT
13060 ATTCGCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (16 bp):
TTTTTGCTCTTTCTTT
Found at i:13053 original size:22 final size:22
Alignment explanation
Indices: 12995--13058 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
12985 CTTTGTCATC
12995 TTTTTGTTCTTTGCTCTTCTCATTG
1 TTTTTG-TCTTTGCT-TT-TCATTG
* *
13020 TTTTTGTTTTTGCTTTTC-TTT
1 TTTTTGTCTTTGCTTTTCATTG
*
13041 TTTTTGCTCTTTGTTTTT
1 TTTTTG-TCTTTGCTTTT
13059 TATTCGCTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.24
22 11 0.32
23 2 0.06
24 7 0.21
25 6 0.18
ACGTcount: A:0.02, C:0.14, G:0.11, T:0.73
Consensus pattern (22 bp):
TTTTTGTCTTTGCTTTTCATTG
Found at i:13284 original size:4 final size:4
Alignment explanation
Indices: 13275--13407 Score: 243
Period size: 4 Copynumber: 33.8 Consensus size: 4
13265 ACAAGAGGTA
*
13275 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13323 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
13371 TATG TATG TATG TATG TATG TA-- TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
13408 ATTTTCTCGA
Statistics
Matches: 125, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
2 2 0.02
4 123 0.98
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:14743 original size:18 final size:17
Alignment explanation
Indices: 14722--14770 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
14712 CTTCTCATTG
14722 TTTTTGTTTTTGCTTTTC
1 TTTTT-TTTTTGCTTTTC
*
14740 -TTTTTTTTTGCTCTTTG
1 TTTTTTTTTTGCT-TTTC
*
14757 TTTTTTCTTTGCTT
1 TTTTTTTTTTGCTT
14771 CTTTTCTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.30
17 8 0.30
18 11 0.41
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (17 bp):
TTTTTTTTTTGCTTTTC
Found at i:14749 original size:16 final size:16
Alignment explanation
Indices: 14723--14770 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
14713 TTCTCATTGT
14723 TTTTGTTTTTGCTTTTC
1 TTTT-TTTTTGCTTTTC
*
14740 TTTTTTTTTGCTCTTTG
1 TTTTTTTTTGCT-TTTC
14757 TTTTTTCTTTGCTT
1 TTTTTT-TTTGCTT
14771 CTTTTCTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 8 0.29
17 14 0.50
18 6 0.21
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.77
Consensus pattern (16 bp):
TTTTTTTTTGCTTTTC
Found at i:14756 original size:29 final size:26
Alignment explanation
Indices: 14724--14787 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 26
14714 TCTCATTGTT
* *
14724 TTTGTTTTTGCTTTTCTTTTTTTTTGCTC
1 TTTGTTTTTGCTTTGC--TTCTTTT-CTC
*
14753 TTTGTTTTTTCTTTGCTTCTTTTCTC
1 TTTGTTTTTGCTTTGCTTCTTTTCTC
14779 TTTGTTTTT
1 TTTGTTTTT
14788 CTGTTCTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.38
27 6 0.19
29 14 0.44
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (26 bp):
TTTGTTTTTGCTTTGCTTCTTTTCTC
Found at i:14767 original size:11 final size:12
Alignment explanation
Indices: 14713--14789 Score: 61
Period size: 12 Copynumber: 6.3 Consensus size: 12
14703 TTCTTTGCTC
*
14713 TTCTCATTGTTT
1 TTCTCTTTGTTT
* * *
14725 TTGTTTTTGCTT
1 TTCTCTTTGTTT
14737 TTCT-TTT-TTT
1 TTCTCTTTGTTT
14747 TTGCTCTTTGTTT
1 TT-CTCTTTGTTT
14760 TT-TCTTTGCTTCTT
1 TTCTCTTTG--T-TT
14774 TTCTCTTTGTTT
1 TTCTCTTTGTTT
14786 TTCT
1 TTCT
14790 GTTCTCTTCG
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
10 4 0.08
11 11 0.21
12 20 0.38
13 7 0.13
14 4 0.08
15 6 0.12
ACGTcount: A:0.01, C:0.16, G:0.09, T:0.74
Consensus pattern (12 bp):
TTCTCTTTGTTT
Found at i:14987 original size:4 final size:4
Alignment explanation
Indices: 14978--15268 Score: 564
Period size: 4 Copynumber: 72.8 Consensus size: 4
14968 ACAAGAGGTA
14978 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
15026 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
15074 TATA TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
15122 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
15170 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
15218 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
15266 TAT
1 TAT
15269 ATTTTCTTGA
Statistics
Matches: 283, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 283 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:16581 original size:24 final size:25
Alignment explanation
Indices: 16545--16597 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
16535 TCATTGTCTG
*
16545 TGCTCTTTGTCA-TCTTTTTGTTCTT
1 TGCTCTTTCTCATTCTTTTTGTT-TT
*
16570 TGCTC-TTCTCATTGTTTTTGTTTT
1 TGCTCTTTCTCATTCTTTTTGTTTT
16594 TGCT
1 TGCT
16598 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.04, C:0.19, G:0.13, T:0.64
Consensus pattern (25 bp):
TGCTCTTTCTCATTCTTTTTGTTTT
Found at i:16619 original size:18 final size:19
Alignment explanation
Indices: 16598--16633 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
16588 TGTTTTTGCT
*
16598 TTTTTTTTTTGC-TCTTTG
1 TTTTTTCTTTGCTTCTTTG
16616 TTTTTTCTTTGCTTCTTT
1 TTTTTTCTTTGCTTCTTT
16634 TCTCTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTTTTCTTTGCTTCTTTG
Found at i:16624 original size:11 final size:12
Alignment explanation
Indices: 16586--16648 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 12
16576 TCTCATTGTT
*
16586 TTTGTTTTTGCTT
1 TTTGTTTTT-CTC
*
16599 TTTTTTTTTGCTC
1 TTTGTTTTT-CTC
16612 TTTGTTTTT-TC
1 TTTGTTTTTCTC
16623 TTTGCTTCTTTTCTC
1 TTTG--T-TTTTCTC
16638 TTTGTTTTTCT
1 TTTGTTTTTCT
16649 GTTCTCTTCG
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
11 6 0.14
12 6 0.14
13 21 0.49
14 4 0.09
15 6 0.14
ACGTcount: A:0.00, C:0.14, G:0.10, T:0.76
Consensus pattern (12 bp):
TTTGTTTTTCTC
Found at i:16657 original size:27 final size:27
Alignment explanation
Indices: 16586--16646 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
16576 TCTCATTGTT
* * *
16586 TTTGTTTTTGCTTT-TTTTTTTTGCTC
1 TTTGTTTTTTCTTTGCTTCTTTTGCTC
16612 TTTGTTTTTTCTTTGCTTCTTTT-CTC
1 TTTGTTTTTTCTTTGCTTCTTTTGCTC
16638 TTTGTTTTT
1 TTTGTTTTT
16647 CTGTTCTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
26 25 0.81
27 6 0.19
ACGTcount: A:0.00, C:0.13, G:0.10, T:0.77
Consensus pattern (27 bp):
TTTGTTTTTTCTTTGCTTCTTTTGCTC
Found at i:17966 original size:14 final size:13
Alignment explanation
Indices: 17921--17963 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
17911 TAAAAAAATG
*
17921 AAATACAGATGCA
1 AAATGCAGATGCA
17934 AAATGCAAAGATGC-
1 AAATGC--AGATGCA
17948 AAATGCAGATGCA
1 AAATGCAGATGCA
17961 AAA
1 AAA
17964 ATGTTGATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 6 0.23
13 8 0.31
14 6 0.23
15 6 0.23
ACGTcount: A:0.53, C:0.14, G:0.19, T:0.14
Consensus pattern (13 bp):
AAATGCAGATGCA
Found at i:23311 original size:20 final size:20
Alignment explanation
Indices: 23288--23329 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
23278 TTTATGAAAG
23288 GATTTAACATTTTTCATGAA
1 GATTTAACATTTTTCATGAA
**
23308 GATTTAATTTTTTTCATGAA
1 GATTTAACATTTTTCATGAA
23328 GA
1 GA
23330 GTATTGATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (20 bp):
GATTTAACATTTTTCATGAA
Found at i:24953 original size:34 final size:34
Alignment explanation
Indices: 24915--24983 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
24905 ACGAACATAC
* *
24915 ACGAACGAATGAAAATATTACCGAACATACACGA
1 ACGAACGAACGAAAATATTACCAAACATACACGA
* * *
24949 ACGAATGAACGAACATATTACCAAACATTCACGA
1 ACGAACGAACGAAAATATTACCAAACATACACGA
24983 A
1 A
24984 TGTAAATGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.49, C:0.22, G:0.13, T:0.16
Consensus pattern (34 bp):
ACGAACGAACGAAAATATTACCAAACATACACGA
Found at i:30451 original size:29 final size:29
Alignment explanation
Indices: 30416--30475 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
30406 ATTTTCACAT
30416 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
30445 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
30474 AA
1 AA
30476 TAATTTAGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.50, C:0.13, G:0.13, T:0.23
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:35459 original size:6 final size:6
Alignment explanation
Indices: 35448--35477 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
35438 TAACACCTTG
35448 TGCATT TGCATT TGCATT TGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT
35478 CTTATTAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
TGCATT
Found at i:41897 original size:214 final size:214
Alignment explanation
Indices: 41521--41920 Score: 728
Period size: 214 Copynumber: 1.9 Consensus size: 214
41511 GTAAACGATT
41521 TAAGTCATTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTAAAAATGAAA
1 TAAGTCATTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTAAAAATGAAA
41586 AACGATGTTTTGAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTT
66 AACGATGTTTTGAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTT
* * *
41651 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGACGCTTAAATCCTTCGGGTCATATGTA
131 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAACGATGAAATCCTTCGGGTCATATGTA
41716 TGCCTTTAGAGCAAGATGA
196 TGCCTTTAGAGCAAGATGA
* *
41735 TAAGTCTTTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAA
1 TAAGTCATTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTAAAAATGAAA
*
41800 AACGATGTTTTGAGAAGATTAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTT
66 AACGATGTTTTGAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTT
* *
41865 ATAAGTCCTTCGGGTCATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTTCGGG
131 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAACGATGAAATCCTTCGGG
41921 CCATCAATAA
Statistics
Matches: 178, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
214 178 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (214 bp):
TAAGTCATTCGGGCCATCCGTAAAACCTTCGGGTAGGATGTTTTCACATGAATTTAAAAATGAAA
AACGATGTTTTGAGAAGATGAAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTCACAATTT
ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAACGATGAAATCCTTCGGGTCATATGTA
TGCCTTTAGAGCAAGATGA
Found at i:41932 original size:42 final size:42
Alignment explanation
Indices: 41870--41961 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
41860 AATTTATAAG
* * *
41870 TCCTTCGGGTCATCAGTAAGTCTTTCGAGCATAATGATGAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATAATAATGAAA
* *
41912 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATAATTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATAATAATGAAA
41954 TCCTTCGG
1 TCCTTCGG
41962 CTAATTTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (42 bp):
TCCTTCGGGCCATCAATAAGTCTTTCGAGCATAATAATGAAA
Found at i:42063 original size:42 final size:41
Alignment explanation
Indices: 42004--42130 Score: 139
Period size: 42 Copynumber: 3.0 Consensus size: 41
41994 AGCAAATCCG
42004 TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCA
1 TCAGTAAGTCTTTCGAGCATGATGAT-AAATCCTTCGGGTCA
* * *
42046 TCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCAGCTCA
1 TCAGTAAGTCTTTCGAGCATGATGA-TAAATCCTTCGGGTCA
** * * * *
42088 TTTGTGAGT-TTCTCGAACAAGATGATAAATCCTTCGAGTCA
1 TCAGTAAGTCTT-TCGAGCATGATGATAAATCCTTCGGGTCA
42129 TC
1 TC
42131 CATAAGACCT
Statistics
Matches: 70, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
41 15 0.21
42 54 0.77
43 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.34
Consensus pattern (41 bp):
TCAGTAAGTCTTTCGAGCATGATGATAAATCCTTCGGGTCA
Found at i:42079 original size:22 final size:22
Alignment explanation
Indices: 42012--42081 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
42002 CGTCAGTAAG
*
42012 TCTTTCGAGCATGATGATGAAA
1 TCTTTCGAGCATGATGATTAAA
* * * *
42034 TCCTTCGGGTCATCA-G--TAAG
1 TCTTTCGAG-CATGATGATTAAA
42054 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGATTAAA
42076 TCTTTC
1 TCTTTC
42082 AGCTCATTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
19 4 0.11
20 10 0.29
22 17 0.49
23 4 0.11
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (22 bp):
TCTTTCGAGCATGATGATTAAA
Found at i:42585 original size:53 final size:53
Alignment explanation
Indices: 42505--42661 Score: 192
Period size: 53 Copynumber: 2.9 Consensus size: 53
42495 AGAATCACAC
*
42505 CAGAAGATTGTTTGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
1 CAGAAGATTATTTGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* ***
42558 CAGAAGATTATTTGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTTTT
1 CAGAAGATTATTTGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
* * * *
42611 TAGAAGATTATTCGAGTTCCTTAATCCCTGAA-CAAGATGGAGC-AGACCCGT
1 CAGAAGATTATTTGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGA-ACCCGT
42662 CGTTTGAAGA
Statistics
Matches: 91, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
53 65 0.71
54 16 0.18
55 10 0.11
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (53 bp):
CAGAAGATTATTTGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAG
Found at i:42672 original size:54 final size:53
Alignment explanation
Indices: 42506--42682 Score: 171
Period size: 53 Copynumber: 3.3 Consensus size: 53
42496 GAATCACACC
* * * ****
42506 AGAAGATTGTTTGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAGC
1 AGAAGATTATTCGAGTTCTAATCCCTGAAGCAAGAGGGAGCGAACCCGTGTTT
* * * *
42559 AGAAGATTATTTGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTTTTT
1 AGAAGATTATTCGAGTTCTAATCCCTGAAGCAAGAGGGAGCGAACCCGTGTTT
*
42612 AGAAGATTATTCGAGTTCCTTAATCCCTGAA-CAAGATGGAGC-AGACCCGTCGTTT
1 AGAAGATTATTCGAGTT-C-TAATCCCTGAAGCAAGAGGGAGCGA-ACCCGT-GTTT
* *
42667 -GAAGATTTTTCAAGTT
1 AGAAGATTATTCGAGTT
42683 TCATTTATCC
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
53 64 0.60
54 30 0.28
55 13 0.12
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (53 bp):
AGAAGATTATTCGAGTTCTAATCCCTGAAGCAAGAGGGAGCGAACCCGTGTTT
Found at i:50317 original size:29 final size:29
Alignment explanation
Indices: 50275--50333 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
50265 ATTTTCACCT
50275 AACTAAAATGATGTAAGCAACGACATCAA
1 AACTAAAATGATGTAAGCAACGACATCAA
* *
50304 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAAATGATGTAAGCAACGACATCAA
50333 A
1 A
50334 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.20
Consensus pattern (29 bp):
AACTAAAATGATGTAAGCAACGACATCAA
Found at i:51753 original size:20 final size:20
Alignment explanation
Indices: 51728--51765 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
51718 AAAATATATT
*
51728 TTCATTTATGTTCGTTTACA
1 TTCATTTATGTTCATTTACA
51748 TTCATTTATGTTCATTTA
1 TTCATTTATGTTCATTTA
51766 TTGTGTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCATTTACA
Found at i:51778 original size:23 final size:23
Alignment explanation
Indices: 51728--51825 Score: 96
Period size: 23 Copynumber: 4.3 Consensus size: 23
51718 AAAATATATT
**
51728 TTCATTTATGTTCGTTTA---CA
1 TTCATTTATGTTCGTTTATTGTG
*
51748 TTCATTTATGTTCATTTATTGTG
1 TTCATTTATGTTCGTTTATTGTG
* *
51771 TTCATTTACGTTCGTTCATTTGTG
1 TTCATTTATGTTCGTTTA-TTGTG
*
51795 TTCGTTTACT-TTCGTTTATTGTG
1 TTCATTTA-TGTTCGTTTATTGTG
51818 TTCATTTA
1 TTCATTTA
51826 CATCCGTTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.27
23 27 0.43
24 19 0.30
ACGTcount: A:0.15, C:0.13, G:0.13, T:0.58
Consensus pattern (23 bp):
TTCATTTATGTTCGTTTATTGTG
Found at i:51783 original size:10 final size:10
Alignment explanation
Indices: 51728--51766 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
51718 AAAATATATT
51728 TTCATTTATG
1 TTCATTTATG
* **
51738 TTCGTTTACA
1 TTCATTTATG
51748 TTCATTTATG
1 TTCATTTATG
51758 TTCATTTAT
1 TTCATTTAT
51767 TGTGTTCATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:51802 original size:24 final size:24
Alignment explanation
Indices: 51766--51843 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 24
51756 TGTTCATTTA
*
51766 TTGTGTTCATTTACGTTCGTTCAT
1 TTGTGTTCATTTACATTCGTTCAT
* * *
51790 TTGTGTTCGTTTACTTTCGTTTA-
1 TTGTGTTCATTTACATTCGTTCAT
*
51813 TTGTGTTCATTTACATCCGTTCAT
1 TTGTGTTCATTTACATTCGTTCAT
51837 TTGTGTT
1 TTGTGTT
51844 TTGTTTATCA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
23 19 0.41
24 27 0.59
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (24 bp):
TTGTGTTCATTTACATTCGTTCAT
Found at i:51826 original size:23 final size:23
Alignment explanation
Indices: 51748--51826 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
51738 TTCGTTTACA
*
51748 TTCATTTA-TGTTCATTTATTGTG
1 TTCATTTACT-TTCGTTTATTGTG
* *
51771 TTCATTTACGTTCGTTCATTTGTG
1 TTCATTTACTTTCGTTTA-TTGTG
*
51795 TTCGTTTACTTTCGTTTATTGTG
1 TTCATTTACTTTCGTTTATTGTG
51818 TTCATTTAC
1 TTCATTTAC
51827 ATCCGTTCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
23 27 0.57
24 20 0.43
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (23 bp):
TTCATTTACTTTCGTTTATTGTG
Found at i:52602 original size:10 final size:10
Alignment explanation
Indices: 52589--52632 Score: 56
Period size: 9 Copynumber: 4.5 Consensus size: 10
52579 ACAAAACACG
52589 TAAAAAATAA
1 TAAAAAATAA
52599 TAAAAAATAA
1 TAAAAAATAA
52609 T-AAAAATAA
1 TAAAAAATAA
*
52618 -ACAAAATAAA
1 TAAAAAAT-AA
52628 TAAAA
1 TAAAA
52633 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 13 0.45
10 13 0.45
11 3 0.10
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:52603 original size:9 final size:9
Alignment explanation
Indices: 52591--52632 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
52581 AAAACACGTA
52591 AAAAATAAT
1 AAAAATAAT
52600 AAAAAATAAT
1 -AAAAATAAT
52610 AAAAATAA-
1 AAAAATAAT
52618 ACAAAATAAAT
1 A-AAAAT-AAT
52629 AAAA
1 AAAA
52633 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 1 0.03
9 13 0.45
10 14 0.48
11 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAAATAAT
Found at i:52613 original size:19 final size:19
Alignment explanation
Indices: 52591--52632 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
52581 AAAACACGTA
52591 AAAAATAATAAAAAAT-AAT
1 AAAAATAA-AAAAAATAAAT
*
52610 AAAAATAAACAAAATAAAT
1 AAAAATAAAAAAAATAAAT
52629 AAAA
1 AAAA
52633 TATTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAATAAAAAAAATAAAT
Found at i:52929 original size:39 final size:37
Alignment explanation
Indices: 52860--52943 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 37
52850 TAATATATAT
* *
52860 AAATAAAT-AAAAATAAAAATAGAATATTAAGAAAAT
1 AAATATATAAAAAATAAAAATAGAATATTAAGAAAAA
* *
52896 ATATATATAAAAACATATAAAATATAATATTAAGAAAAA
1 AAATATATAAAAA-ATA-AAAATAGAATATTAAGAAAAA
52935 AAATATATA
1 AAATATATA
52944 TATAGCAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
36 6 0.15
37 4 0.10
38 3 0.08
39 27 0.68
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (37 bp):
AAATATATAAAAAATAAAAATAGAATATTAAGAAAAA
Found at i:52933 original size:16 final size:16
Alignment explanation
Indices: 52843--52922 Score: 62
Period size: 16 Copynumber: 5.1 Consensus size: 16
52833 AAAATAAAGT
52843 AAAAATATAATATATA
1 AAAAATATAATATATA
*
52859 TAAATAA-ATAA-AAAT-
1 -AAA-AATATAATATATA
*
52874 AAAAATAGAATAT-TA
1 AAAAATATAATATATA
52889 AGAAAATAT-ATATATA
1 A-AAAATATAATATATA
*
52905 AAAACATATAAAATATA
1 AAAA-ATATAATATATA
52922 A
1 A
52923 TATTAAGAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
13 2 0.04
14 7 0.14
15 9 0.18
16 16 0.32
17 14 0.28
18 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAAATATAATATATA
Found at i:53035 original size:4 final size:4
Alignment explanation
Indices: 53021--53054 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
53011 TAAAAATAGT
53021 ATAA TATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
53055 AGAGGAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:53053 original size:40 final size:40
Alignment explanation
Indices: 53009--53103 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 40
52999 AGATATATAT
53009 AATAAAAATAGTATA-ATA-TAAATAAATAAATAAATAAATA
1 AATAAAAATAGTATATATAGTAAATAAATAAA-AAA-AAATA
* * *
53049 AAT-AAAAGAGGA-ATATAGTAAATAAATAAAAAAATATA
1 AATAAAAATAGTATATATAGTAAATAAATAAAAAAAAATA
*
53087 ATTAAAAATA-TATATAT
1 AATAAAAATAGTATATAT
53104 GGGAGACGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
38 8 0.18
39 22 0.49
40 15 0.33
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.27
Consensus pattern (40 bp):
AATAAAAATAGTATATATAGTAAATAAATAAAAAAAAATA
Found at i:66121 original size:10 final size:10
Alignment explanation
Indices: 66108--66149 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
66098 CACGTAAAAA
66108 AAATAATAAT
1 AAATAATAAT
66118 AAATAATAAT
1 AAATAATAAT
66128 AAA-AATAA-
1 AAATAATAAT
*
66136 AAAAAATGAAT
1 AAATAAT-AAT
66147 AAA
1 AAA
66150 ATGTTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 3 0.10
9 8 0.28
10 15 0.52
11 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (10 bp):
AAATAATAAT
Found at i:66134 original size:22 final size:22
Alignment explanation
Indices: 66106--66148 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
66096 AACACGTAAA
*
66106 AAAAATAATAATAAAT-AATAAT
1 AAAAATAA-AAAAAATGAATAAT
66128 AAAAATAAAAAAAATGAATAA
1 AAAAATAAAAAAAATGAATAA
66149 AATGTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (22 bp):
AAAAATAAAAAAAATGAATAAT
Found at i:66147 original size:19 final size:19
Alignment explanation
Indices: 66112--66150 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
66102 TAAAAAAAAT
*
66112 AATAATAAATAATAATAAA
1 AATAATAAAAAATAATAAA
66131 AATAA-AAAAAATGAATAAA
1 AATAATAAAAAAT-AATAAA
66150 A
1 A
66151 TGTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (19 bp):
AATAATAAAAAATAATAAA
Found at i:66409 original size:18 final size:18
Alignment explanation
Indices: 66386--66451 Score: 78
Period size: 18 Copynumber: 3.5 Consensus size: 18
66376 AAATTAAAAC
*
66386 AAAAATAGAATATTAAGA
1 AAAAATATAATATTAAGA
*
66404 AAAAATATATATATAAATGTA
1 AAAAATATA-ATATTAA-G-A
*
66425 TAAAATATAATATTAAGA
1 AAAAATATAATATTAAGA
66443 AAAAATATA
1 AAAAATATA
66452 TATACATAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
18 17 0.43
19 7 0.17
20 7 0.17
21 9 0.22
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
AAAAATATAATATTAAGA
Found at i:66497 original size:2 final size:2
Alignment explanation
Indices: 66485--66531 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
66475 TTAATACATC
* *
66485 TA TA CA TA TA TA TA TA TA TA TA TA TA TA -A TA AA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66525 TA -A TA TA
1 TA TA TA TA
66532 AATAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:66532 original size:10 final size:10
Alignment explanation
Indices: 66485--66540 Score: 55
Period size: 12 Copynumber: 5.5 Consensus size: 10
66475 TTAATACATC
66485 TATACATATATA
1 TATA-ATATA-A
66497 TATATATATATA
1 TATA-ATATA-A
66509 TATAATA-AA
1 TATAATATAA
66518 TATAATATAA
1 TATAATATAA
66528 TATAA-ATAA
1 TATAATATAA
66537 -ATAA
1 TATAA
66541 AGAAAGAGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
8 4 0.10
9 12 0.29
10 8 0.19
11 3 0.07
12 15 0.36
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
TATAATATAA
Found at i:72383 original size:28 final size:28
Alignment explanation
Indices: 72331--72384 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
72321 GGTCTTTTTA
* *
72331 TTTATTTATTATTATTAATTATTATATG
1 TTTATCTATTATTATTAAATATTATATG
72359 TTTATCTATTATTATTATAAT-TTATA
1 TTTATCTATTATTATTA-AATATTATA
72385 ATTTACATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTATCTATTATTATTAAATATTATATG
Found at i:78603 original size:19 final size:19
Alignment explanation
Indices: 78563--78606 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
78553 ATGTATACAA
**
78563 TAAAGCTGAGCTATTCTGC
1 TAAAGCTGAGCTATTCCAC
78582 TAAAGCTGAGCTATTCCAC
1 TAAAGCTGAGCTATTCCAC
78601 TAAAGC
1 TAAAGC
78607 GATTGGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (19 bp):
TAAAGCTGAGCTATTCCAC
Found at i:82879 original size:30 final size:30
Alignment explanation
Indices: 82820--82922 Score: 145
Period size: 30 Copynumber: 3.4 Consensus size: 30
82810 CCCGAAGGAC
* *
82820 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
82849 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
82879 CTGTCCAGAGGTCATAAAGATCCTCGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGT-AA
* *
82910 CTGTCCATAGGTC
1 CTATCCAGAGGTC
82923 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
29 19 0.28
30 35 0.51
31 14 0.21
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:82962 original size:31 final size:31
Alignment explanation
Indices: 82904--83035 Score: 133
Period size: 31 Copynumber: 4.2 Consensus size: 31
82894 AAAGATCCTC
* * **
82904 GGTAAACTGTCCATAGGTCCCGAAGAACCCA
1 GGTAAACTGTCCATATGTTCCGAAGAACATA
**
82935 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCGAAGAACATA
* *
82966 AGTATACTGTCCATATG-TCTCGAA-AGACATA
1 GGTAAACTGTCCATATGTTC-CGAAGA-ACATA
*
82997 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT-AAACTGTCCATATGTTCCGAAGAACATA
*
83029 GGCAAAC
1 GGTAAAC
83036 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
30 3 0.04
31 53 0.65
32 23 0.28
33 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCGAAGAACATA
Found at i:84328 original size:21 final size:21
Alignment explanation
Indices: 84298--84342 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
84288 ATTCTGTCGT
* *
84298 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
84319 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
84340 TTG
1 TTG
84343 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:93413 original size:2 final size:2
Alignment explanation
Indices: 93408--93447 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
93398 GTGCAAAAAA
*
93408 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93448 TAAAATGTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Done.