Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004672.1 Hibiscus syriacus cultivar Beakdansim tig00010475_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: 62225
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2237 original size:33 final size:33
Alignment explanation
Indices: 2189--2280 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
2179 GGCATAATTC
*
2189 ATGCCAATAATGCACCCATATGCATTATTCTTT
1 ATGCCGATAATGCACCCATATGCATTATTCTTT
*
2222 ATGCTGATAATGCACCCATATGCATTATTCTTT
1 ATGCCGATAATGCACCCATATGCATTATTCTTT
*
2255 ATGCCGATGATGCACCCATATGCATT
1 ATGCCGATAATGCACCCATATGCATT
2281 TCAGCTAGGG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (33 bp):
ATGCCGATAATGCACCCATATGCATTATTCTTT
Found at i:2413 original size:43 final size:45
Alignment explanation
Indices: 2331--2423 Score: 163
Period size: 44 Copynumber: 2.1 Consensus size: 45
2321 GCATTATTTT
*
2331 TATTCATTCATTTAGAGTAGTTCATACTCTAAAATTCATTC-TAA
1 TATTCATTCATTTAGAGTAGTTCATACTCTAAAACTCATTCATAA
2375 TATTCATTCATTTAGAG-AGTTCATACTCTAAAACTCATTCATAA
1 TATTCATTCATTTAGAGTAGTTCATACTCTAAAACTCATTCATAA
2419 TATTC
1 TATTC
2424 TTTCCATACA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 22 0.47
44 25 0.53
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.42
Consensus pattern (45 bp):
TATTCATTCATTTAGAGTAGTTCATACTCTAAAACTCATTCATAA
Found at i:5193 original size:19 final size:19
Alignment explanation
Indices: 5169--5207 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
5159 GATGCAAATG
5169 AAAAAAATGAAA-GAAAAC
1 AAAAAAATGAAAGGAAAAC
5187 AAAAAAATGAAAGGAAAAC
1 AAAAAAATGAAAGGAAAAC
5206 AA
1 AA
5208 GTTAGTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.77, C:0.05, G:0.13, T:0.05
Consensus pattern (19 bp):
AAAAAAATGAAAGGAAAAC
Found at i:7092 original size:15 final size:14
Alignment explanation
Indices: 7074--7120 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
7064 ATCATATGAA
*
7074 ATGTGATAGAGAGCT
1 ATGTGATA-AGAACT
7089 ATGTGA-AAGAACT
1 ATGTGATAAGAACT
*
7102 ATGTGATATGAA-T
1 ATGTGATAAGAACT
7115 ATGTGA
1 ATGTGA
7121 ATGTATAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 18 0.62
14 5 0.17
15 6 0.21
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (14 bp):
ATGTGATAAGAACT
Found at i:7526 original size:2 final size:2
Alignment explanation
Indices: 7519--7560 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
7509 ATGTACATGA
7519 AT AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7559 AT
1 AT
7561 GAATGAATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9592 original size:14 final size:14
Alignment explanation
Indices: 9573--9609 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
9563 AACATTAGAA
9573 GATATGTTCTTATT
1 GATATGTTCTTATT
9587 GATATGTTCTTATT
1 GATATGTTCTTATT
9601 GATATGTTC
1 GATATGTTC
9610 AATGAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (14 bp):
GATATGTTCTTATT
Found at i:11656 original size:2 final size:2
Alignment explanation
Indices: 11649--11680 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11639 ATGTACATGA
11649 AT AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11681 GAATGAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13107 original size:28 final size:28
Alignment explanation
Indices: 13049--13107 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
13039 ATCAAAGAGG
* **
13049 GAAAAGAAAAAAAATAAAACTACATTGA
1 GAAAAGAAAAAAAATAAAAATACATAAA
*
13077 GAAAATAACAAAAAATAAAAATA-ATAAA
1 GAAAAGAA-AAAAAATAAAAATACATAAA
13105 GAA
1 GAA
13108 GGTTAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.14
Consensus pattern (28 bp):
GAAAAGAAAAAAAATAAAAATACATAAA
Found at i:13175 original size:5 final size:5
Alignment explanation
Indices: 13165--13196 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
13155 GGAAAATATT
13165 AAATA AAATA AAATA AAATA AAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAA
13197 ATGAAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:13787 original size:5 final size:5
Alignment explanation
Indices: 13779--14431 Score: 1094
Period size: 5 Copynumber: 133.0 Consensus size: 5
13769 TGTTAATAAC
13779 AATAT AATA- ATATAT AATAT AATAT AATAT AATAT -ATAT -ATAT AATAT
1 AATAT AATAT A-ATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
13827 AATAT AATAT AATAT -A-AT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
13875 -A-AT AATAT AATAT -ATAT -ATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
13921 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -A-AT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
13969 AATATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 -A-ATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
14021 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
14071 AATAT AATAT AATAT -ATAT AATAT AATAT AATAT AATAT ATATAT ATATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT A-ATAT
14122 AATAT AATAT -ATAT AATAT AATAT AATAT AATAT AATAT -ATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
14170 AATAT AATAT AATAT AATAT AATAT AATAT ATATAT AATAT -ATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT
14220 AATAT AATAT AATAT AATAT AATAT AATAT -ATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
14269 AATATAT AATAT AATAT AATAT AATAT AATAT -A-AT AATAT AATAT AATAT
1 -A-ATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
14319 AATAT AATAT AATAT AATAT -A-AT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
14367 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
14417 AATAT AATAT AATAT
1 AATAT AATAT AATAT
14432 GTATACTGTA
Statistics
Matches: 623, Mismatches: 0, Indels: 50
0.93 0.00 0.07
Matches are distributed among these distances:
3 10 0.02
4 47 0.08
5 537 0.86
6 21 0.03
7 8 0.01
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
AATAT
Found at i:14661 original size:25 final size:23
Alignment explanation
Indices: 14599--14661 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
14589 TTCAAAAATA
*
14599 TTTTAAAAACTATATATTATATG
1 TTTTCAAAACTATATATTATATG
14622 TTTTCAAAACTATATATTATATG
1 TTTTCAAAACTATATATTATATG
14645 TTTTCCAAAACTGATAT
1 TTTT-CAAAACT-ATAT
14662 TTAAAAAACT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
23 26 0.70
24 7 0.19
25 4 0.11
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.46
Consensus pattern (23 bp):
TTTTCAAAACTATATATTATATG
Found at i:14670 original size:39 final size:39
Alignment explanation
Indices: 14622--14781 Score: 166
Period size: 39 Copynumber: 4.0 Consensus size: 39
14612 ATATTATATG
*
14622 TTTTCAAAACTATATA-T-TATATGTTTTCCAAAACTGATA
1 TTTTAAAAACTATATATTATATATGTTTT-CAAAACT-ATA
* * *
14661 TTTAAAAAACTATATATTATATATGTTTTCAAAAATATG
1 TTTTAAAAACTATATATTATATATGTTTTCAAAACTATA
* * *
14700 TTTTTAAAACTATATA-T-TATATGTTTTCCAAAACCGTTTTTT
1 TTTTAAAAACTATATATTATATATGTTTT-CAAAA-C---TATA
14742 TTTTAAAAACTATATATTATATATGTTTTCAAAACTATA
1 TTTTAAAAACTATATATTATATATGTTTTCAAAACTATA
14781 T
1 T
14782 ATTATACGTT
Statistics
Matches: 100, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
37 10 0.10
38 6 0.06
39 33 0.33
40 7 0.07
41 10 0.10
42 18 0.18
43 6 0.06
44 10 0.10
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.47
Consensus pattern (39 bp):
TTTTAAAAACTATATATTATATATGTTTTCAAAACTATA
Found at i:14716 original size:78 final size:80
Alignment explanation
Indices: 14617--14775 Score: 250
Period size: 78 Copynumber: 2.0 Consensus size: 80
14607 ACTATATATT
14617 ATATGTTTTCAAAACTATATATTATATGTTTTCCAAAA-C-TGATATTTAAAAAACTATATATTA
1 ATATGTTTTCAAAACTATATATTATATGTTTTCCAAAACCGTGATATTTAAAAAACTATATATTA
14680 TATATGTTTTCAAAA
66 TATATGTTTTCAAAA
* ** * *
14695 ATATGTTTTTAAAACTATATATTATATGTTTTCCAAAACCGTTTTTTTTTTAAAAACTATATATT
1 ATATGTTTTCAAAACTATATATTATATGTTTTCCAAAACCG-TGATATTTAAAAAACTATATATT
14760 ATATATGTTTTCAAAA
65 ATATATGTTTTCAAAA
14776 CTATATATTA
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
78 37 0.51
79 1 0.01
81 35 0.48
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (80 bp):
ATATGTTTTCAAAACTATATATTATATGTTTTCCAAAACCGTGATATTTAAAAAACTATATATTA
TATATGTTTTCAAAA
Found at i:14725 original size:23 final size:23
Alignment explanation
Indices: 14695--14799 Score: 94
Period size: 23 Copynumber: 4.6 Consensus size: 23
14685 GTTTTCAAAA
*
14695 ATATGTTTTTAAAACTATATATT
1 ATATGTTTTCAAAACTATATATT
**
14718 ATATGTTTTCCAAAACCGT-T-TT
1 ATATGTTTT-CAAAACTATATATT
*
14740 -T-T-TTTTAAAAACTATATATTAT
1 ATATGTTTTCAAAACTATATA-T-T
14762 ATATGTTTTCAAAACTATATATT
1 ATATGTTTTCAAAACTATATATT
*
14785 ATACGTTTTCTAAAA
1 ATATGTTTTC-AAAA
14800 ATATTTTCAA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
18 6 0.09
19 5 0.08
20 1 0.02
21 2 0.03
22 3 0.05
23 21 0.32
24 12 0.18
25 15 0.23
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (23 bp):
ATATGTTTTCAAAACTATATATT
Found at i:14800 original size:25 final size:27
Alignment explanation
Indices: 14740--14800 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 27
14730 AAACCGTTTT
* *
14740 TTTTTTAAAAACTATATATTATATATG
1 TTTTCTAAAAACTATATATTATATACG
14767 TTTTC--AAAACTATATA-T-TATACG
1 TTTTCTAAAAACTATATATTATATACG
14790 TTTTCTAAAAA
1 TTTTCTAAAAA
14801 TATTTTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
23 10 0.33
24 1 0.03
25 15 0.50
27 4 0.13
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (27 bp):
TTTTCTAAAAACTATATATTATATACG
Found at i:17963 original size:18 final size:18
Alignment explanation
Indices: 17940--17979 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17930 TTTTAATGAT
17940 GGTGATAGTCATTGGTTA
1 GGTGATAGTCATTGGTTA
* **
17958 GGTGATGGTTGTTGGTTA
1 GGTGATAGTCATTGGTTA
17976 GGTG
1 GGTG
17980 GTCATGAGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.42, T:0.40
Consensus pattern (18 bp):
GGTGATAGTCATTGGTTA
Found at i:18472 original size:13 final size:13
Alignment explanation
Indices: 18454--18478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18444 GCCTACAAAA
18454 TGTATTAATAATT
1 TGTATTAATAATT
18467 TGTATTAATAAT
1 TGTATTAATAAT
18479 GATAATAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TGTATTAATAATT
Found at i:18478 original size:3 final size:3
Alignment explanation
Indices: 18472--18508 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
18462 TAATTTGTAT
*
18472 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
18509 TTTTTAAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:18774 original size:40 final size:40
Alignment explanation
Indices: 18699--18775 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
18689 GTCATTTTTA
* *
18699 GGATGACGCTGCTCCTACGTGATGATGAGATCTGGTTGGT
1 GGATGACACTGCTCCTACGTGATGAGGAGATCTGGTTGGT
*
18739 GGATGACACTGTTCCTACGTGATGAGGACGA-CTGGTT
1 GGATGACACTGCTCCTACGTGATGAGGA-GATCTGGTT
18776 ATCTAAGGGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 31 0.94
41 2 0.06
ACGTcount: A:0.19, C:0.18, G:0.34, T:0.29
Consensus pattern (40 bp):
GGATGACACTGCTCCTACGTGATGAGGAGATCTGGTTGGT
Found at i:19140 original size:66 final size:66
Alignment explanation
Indices: 19005--19349 Score: 405
Period size: 66 Copynumber: 5.2 Consensus size: 66
18995 AGGGATAATG
* * * *
19005 GTTTCAAGAGAAACTGTCTGAAGAGAGA-AAAACTTGTTTCAAGGGAAAC-ATAATCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAT-CTCAAAGA-TT
**
19068 TAT
64 GGT
* * * * *
19071 GTTTCAAGAGAAATTGTCTCAAGGGATATAAAATTTATTTCAAGGGAAACAATCTCAAAGGTTGG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTGG
19136 T
66 T
*
19137 GTTTCAAGAGAAACTGACTCAAGGGAGACAAAACTTT-TTTCAAGGGAAAC-ATACTCAAAGATT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACAAT-CTCAAAGATT
*
19200 GGC
64 GGT
* * *
19203 ATTTCAAGAGAAACTGTCTCAAAGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAA-AGTTG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGA-TTG
19267 GT
65 GT
*
19269 GTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTTGTTTCAAGGGAAACAGA-CTCAAAGATT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCAAGGGAAACA-ATCTCAAAGATT
**
19333 TTT
64 GGT
*
19336 GTTTCAATAGAAAC
1 GTTTCAAGAGAAAC
19350 ATACTCAAAG
Statistics
Matches: 240, Mismatches: 29, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
65 5 0.02
66 163 0.68
67 68 0.28
68 4 0.02
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (66 bp):
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGATTGG
T
Found at i:19244 original size:132 final size:132
Alignment explanation
Indices: 19005--19332 Score: 471
Period size: 132 Copynumber: 2.5 Consensus size: 132
18995 AGGGATAATG
* * * * **
19005 GTTTCAAGAGAAACTGTCTGAAGAGAGA-AAAACTTGTTTCAAGGGAAACATAATCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTTTTCAAGGGAAACATACTCAAAGATTGC
* * * * * *
19069 ATGTTTCAAGAGAAATTGTCTCAAGGGATATAAAATTTATTTCAAGGGAAACAATCTCAAAGGTT
66 A-GTTTCAAGAGAAACTGTCTCAAAGGAGACAAAACTTATTTCAAGGGAAACAATCTCAAAAGTT
19134 GGT
130 GGT
*
19137 GTTTCAAGAGAAACTGACTCAAGGGAGACAAAACTTTTTTCAAGGGAAACATACTCAAAGATTGG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTTTTCAAGGGAAACATACTCAAAGATT-G
*
19202 CA-TTTCAAGAGAAACTGTCTCAAAGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAAGTT
65 CAGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAACTTATTTCAAGGGAAACAATCTCAAAAGTT
19266 GGT
130 GGT
* *
19269 GTTTCAAGAGAAATTGTCTCAAGGGAGACAAAACTTTGTTTCAAGGGAAACAGACTCAAAGATT
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTT-TTTCAAGGGAAACATACTCAAAGATT
19333 TTTGTTTCAA
Statistics
Matches: 176, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
132 118 0.67
133 57 0.32
134 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (132 bp):
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTTTTCAAGGGAAACATACTCAAAGATTGC
AGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAACTTATTTCAAGGGAAACAATCTCAAAAGTTG
GT
Found at i:19337 original size:30 final size:30
Alignment explanation
Indices: 19303--19359 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
19293 GAGACAAAAC
*
19303 TTTGTTTCAAGGGAAACAGACTCAAAGATT
1 TTTGTTTCAAGAGAAACAGACTCAAAGATT
* *
19333 TTTGTTTCAATAGAAACATACTCAAAG
1 TTTGTTTCAAGAGAAACAGACTCAAAG
19360 TTTATCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (30 bp):
TTTGTTTCAAGAGAAACAGACTCAAAGATT
Found at i:19840 original size:32 final size:32
Alignment explanation
Indices: 19799--19862 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
19789 TTCACTTCAG
*
19799 GATGTTGAATCTCCAAATATGCCCCAACATTC
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
19831 GATGTTGAATCTCCAAAGATGCCCCAACATTC
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
19863 ATCATTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTC
Found at i:20919 original size:12 final size:12
Alignment explanation
Indices: 20902--20944 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
20892 TCTTTTTTTC
20902 CTTTTTTCTTTG
1 CTTTTTTCTTTG
20914 CTTTTTTCTTCTTAG
1 CTTTTTTC-T-TT-G
*
20929 CTTTTCTCTTTG
1 CTTTTTTCTTTG
20941 CTTT
1 CTTT
20945 GATTTTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 13 0.48
13 3 0.11
14 3 0.11
15 8 0.30
ACGTcount: A:0.02, C:0.21, G:0.07, T:0.70
Consensus pattern (12 bp):
CTTTTTTCTTTG
Found at i:26595 original size:13 final size:13
Alignment explanation
Indices: 26577--26601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26567 GCCTACAAAA
26577 TGTATTAATAATT
1 TGTATTAATAATT
26590 TGTATTAATAAT
1 TGTATTAATAAT
26602 AATAATAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (13 bp):
TGTATTAATAATT
Found at i:26601 original size:3 final size:3
Alignment explanation
Indices: 26595--26634 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
26585 TAATTTGTAT
26595 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
26635 TTTTAAGATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:27681 original size:30 final size:30
Alignment explanation
Indices: 27647--27717 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
27637 TATCTTAATT
27647 AAAAATTAAAATATTAAA-ATTAAAAATG-AA
1 AAAAATTAAAA-ATTAAAGATT-AAAATGTAA
27677 AAAAATTAAAAATTAAAGATTAAAATGTAA
1 AAAAATTAAAAATTAAAGATTAAAATGTAA
27707 AAAAATTAAAA
1 AAAAATTAAAA
27718 CCACACTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
29 12 0.31
30 27 0.69
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.25
Consensus pattern (30 bp):
AAAAATTAAAAATTAAAGATTAAAATGTAA
Found at i:27717 original size:7 final size:7
Alignment explanation
Indices: 27643--27701 Score: 66
Period size: 7 Copynumber: 8.1 Consensus size: 7
27633 ATTATATCTT
27643 AATTAAA
1 AATTAAA
27650 AATTAAA
1 AATTAAA
27657 ATATT-AA
1 A-ATTAAA
27664 AATTAAA
1 AATTAAA
*
27671 AATGAAAAA
1 AAT--TAAA
27680 AATTAAA
1 AATTAAA
27687 AATTAAA
1 AATTAAA
*
27694 GATTAAA
1 AATTAAA
27701 A
1 A
27702 TGTAAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 3 0.07
7 32 0.73
8 3 0.07
9 6 0.14
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (7 bp):
AATTAAA
Found at i:29438 original size:16 final size:16
Alignment explanation
Indices: 29419--29450 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29409 TTAGTAATCT
29419 CAATTTTAATTAATTA
1 CAATTTTAATTAATTA
29435 CAATTTTAATTAATTA
1 CAATTTTAATTAATTA
29451 AGTATAGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
CAATTTTAATTAATTA
Found at i:41565 original size:15 final size:15
Alignment explanation
Indices: 41545--41621 Score: 154
Period size: 15 Copynumber: 5.1 Consensus size: 15
41535 TAATGGAGGT
41545 CTTCCACGGAAGCTG
1 CTTCCACGGAAGCTG
41560 CTTCCACGGAAGCTG
1 CTTCCACGGAAGCTG
41575 CTTCCACGGAAGCTG
1 CTTCCACGGAAGCTG
41590 CTTCCACGGAAGCTG
1 CTTCCACGGAAGCTG
41605 CTTCCACGGAAGCTG
1 CTTCCACGGAAGCTG
41620 CT
1 CT
41622 CTCAACCTGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 62 1.00
ACGTcount: A:0.19, C:0.34, G:0.26, T:0.21
Consensus pattern (15 bp):
CTTCCACGGAAGCTG
Found at i:42804 original size:13 final size:13
Alignment explanation
Indices: 42786--42822 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
42776 TATTGGTATT
*
42786 GAAATATGATTCA
1 GAAATATGAATCA
42799 GAAATATGAATCA
1 GAAATATGAATCA
42812 GAAATATGAAT
1 GAAATATGAAT
42823 GTTGCTTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.27
Consensus pattern (13 bp):
GAAATATGAATCA
Found at i:47093 original size:68 final size:69
Alignment explanation
Indices: 46966--47444 Score: 596
Period size: 68 Copynumber: 6.9 Consensus size: 69
46956 AACTTGCTTT
* * * * *
46966 AAGAGAAATTGTCTCAAGTGATACAAAACTTTGTTTCAAGGGAAACAATCTC-AATGTTTTTATG
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTTTATG
47030 TTTC
66 TTTC
* * *
47034 AAGAGAAACTGCCTCAAGATAGACAAAAC-TTGTCTCAAGAGAAACAATCTCAAAGG-TTTTATG
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTTTATG
47097 TTTC
66 TTTC
* *
47101 AAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTTTTTT
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGG---TTTTT
47166 ATGTTTC
63 ATGTTTC
* *
47173 AAGAGAAACTGTCTCAAGCA-AGA-AACAAC-TTGTTTCAAGAGAAACAATCTCAATGATTTATC
1 AAGAGAAACTGTCTCAAG-AGAGACAA-AACTTTGTTTCAAGAGAAACAATCTCAAAG-GTT-T-
*
47235 AATTTTGTTTC
61 --TTATGTTTC
**
47246 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTGAGAGAAACAATCTCAAAGGTTTTTTTA
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGG--TTTTTA
47311 TGTTTC
64 TGTTTC
* * * * *
47317 AAGAGAAACTGTCTCAAGCGAAACACAACTTTGTTTCAAGGGAAACAATCTC-AATGTTTTTATG
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTTTATG
47381 TTTC
66 TTTC
* *
47385 AAGAGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGAGAAAAAATCTTAAAGGTTTT
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTT
47445 ATCAATTTTA
Statistics
Matches: 355, Mismatches: 37, Indels: 38
0.83 0.09 0.09
Matches are distributed among these distances:
67 76 0.21
68 97 0.27
69 2 0.01
70 4 0.01
71 80 0.23
72 35 0.10
73 33 0.09
74 26 0.07
75 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (69 bp):
AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTTTATG
TTTC
Found at i:47153 original size:37 final size:37
Alignment explanation
Indices: 47028--47434 Score: 141
Period size: 37 Copynumber: 11.5 Consensus size: 37
47018 AATGTTTTTA
*** *
47028 TGTTTCAAGAGAAACTGCCTCAAGATAGACAAAAC-T
1 TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
* **
47064 TGTCTCAAGAGAAACAATCTCAA-AG-G-----TTTT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
***
47094 ATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 -TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
* ******
47132 TGTTTCGAGAGAAACAATCTCAA-AG-G-TTTTTTTT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
**
47166 ATGTTTCAAGAGAAACTGTCTCAAGCA-AGA-AACAAC-T
1 -TGTTTCAAGAGAAACAATCTCAAG-AGAGACAA-AACTT
*** *
47203 TGTTTCAAGAGAAACAATCTCAATGATTTATC--AATTT
1 TGTTTCAAGAGAAACAATCTCAA-GAGAGA-CAAAACTT
**
47240 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
** *****
47277 TGTTTTGAGAGAAACAATCTCAA-AG-G--TTTTTTT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
** * * *
47310 ATGTTTCAAGAGAAACTGTCTCAAGCGAAACACAACTT
1 -TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
* * ***
47348 TGTTTCAAGGGAAACAATCTC-A-A-TG----TTTTT
1 TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
**
47378 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC-T
1 -TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
*
47415 TGTTTCAAGAGAAAAAATCT
1 TGTTTCAAGAGAAACAATCT
47435 TAAAGGTTTT
Statistics
Matches: 255, Mismatches: 81, Indels: 70
0.63 0.20 0.17
Matches are distributed among these distances:
30 3 0.01
31 37 0.15
32 3 0.01
33 4 0.02
34 23 0.09
35 25 0.10
36 68 0.27
37 88 0.35
38 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGAGAAACAATCTCAAGAGAGACAAAACTT
Found at i:47214 original size:36 final size:36
Alignment explanation
Indices: 47167--47264 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
47157 GTTTTTTTTA
47167 TGTTTCAAGAGAAACTGTCTCAAGCAAGAAACAA-CT
1 TGTTTCAAGAGAAACTGTCTCAAG-AAGAAACAATCT
** *** * *
47203 TGTTTCAAGAGAAACAATCTCAATGATTTATCAATTT
1 TGTTTCAAGAGAAACTGTCTCAA-GAAGAAACAATCT
47240 TGTTTCAAGAGAAACTGTCTCAAGA
1 TGTTTCAAGAGAAACTGTCTCAAGA
47265 GAGACAAAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
36 28 0.55
37 23 0.45
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAAGAAACAATCT
Found at i:47216 original size:139 final size:138
Alignment explanation
Indices: 46966--47444 Score: 648
Period size: 139 Copynumber: 3.4 Consensus size: 138
46956 AACTTGCTTT
* * * * *
46966 AAGAGAAATTGTCTCAAGTGATACAAAACTTTGTTTCAAGGGAAACAATCTC-AA--TGTTTTTA
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTTTTTA
* * * *
47028 TGTTTCAAGAGAAACTGCCTCAAG-ATAGACAA-AACTTGTCTCAAGAGAAACAATCTCAAAGGT
66 TGTTTCAAGAGAAACTGTCTCAAGCA-AGA-AACAACTTGTTTCAAGAGAAACAATCTCAATGAT
47091 TTTATGTTTC
129 TTTATGTTTC
* *
47101 AAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTTTTTT
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGG-TTTTTTT
47166 ATGTTTCAAGAGAAACTGTCTCAAGCAAGAAACAACTTGTTTCAAGAGAAACAATCTCAATGATT
65 ATGTTTCAAGAGAAACTGTCTCAAGCAAGAAACAACTTGTTTCAAGAGAAACAATCTCAATGATT
47231 TATCAATTTTGTTTC
130 T-T--A---TGTTTC
**
47246 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTGAGAGAAACAATCTCAAAGGTTTTTTTA
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTTTTTA
* * *
47311 TGTTTCAAGAGAAACTGTCTCAAGCGAA-ACACAACTTTGTTTCAAGGGAAACAATCTCAATGTT
66 TGTTTCAAGAGAAACTGTCTCAAGC-AAGAAACAAC-TTGTTTCAAGAGAAACAATCTCAATGAT
47375 TTTATGTTTC
129 TTTATGTTTC
* *
47385 AAGAGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGAGAAAAAATCTTAAAGGTTTT
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTT
47445 ATCAATTTTA
Statistics
Matches: 312, Mismatches: 18, Indels: 25
0.88 0.05 0.07
Matches are distributed among these distances:
135 48 0.15
136 2 0.01
138 29 0.09
139 98 0.31
140 2 0.01
142 2 0.01
144 40 0.13
145 91 0.29
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (138 bp):
AAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTTTTTA
TGTTTCAAGAGAAACTGTCTCAAGCAAGAAACAACTTGTTTCAAGAGAAACAATCTCAATGATTT
TATGTTTC
Found at i:47389 original size:212 final size:209
Alignment explanation
Indices: 46966--47467 Score: 635
Period size: 212 Copynumber: 2.4 Consensus size: 209
46956 AACTTGCTTT
* * * *
46966 AAGAGAAATTGTCTCAAGTGATACAAAACTTTGTTTCAAGGGAAACAATCTCAATG-TT-T---T
1 AAGAGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGAGAAACAATCTCAATGTTTATCAAT
* *
47026 TATGTTTCAAGAGAAACTGCCTCAAGATAGACAAAACTTGTCTCAAGAGAAACAATCTCAAAGGT
65 TTTGTTTCAAGAGAAACTGCCTCAAGAGAGACAAAACTTGTCTCAAGAGAAACAATCTCAAAGGT
* * *
47091 TTTATGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAA
130 TTTATGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAACTTTGTTTCAAGAGAAACAATCTCAAA
*
47156 GGTTTTTTTTATGTTTC
195 -G-TGTTTTTATGTTTC
47173 AAGAGAAACTGTCTCAAGCA-AGA-AACAACTTGTTTCAAGAGAAACAATCTCAATGATTTATCA
1 AAGAGAAACTGTCTCAAG-AGAGACAA-AACTTGTTTCAAGAGAAACAATCTCAATG-TTTATCA
* * **
47236 ATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTGAGAGAAACAATCTCAAA
63 ATTTTGTTTCAAGAGAAACTGCCTCAAGAGAGACAAAAC-TTGTCTCAAGAGAAACAATCTCAAA
* * *
47301 GGTTTTTTTATGTTTCAAGAGAAACTGTCTCAAGCGAAACACAACTTTGTTTCAAGGGAAACAAT
127 GG---TTTTATGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAACTTTGTTTCAAGAGAAACAAT
47366 CTC-AA-TGTTTTTATGTTTC
189 CTCAAAGTGTTTTTATGTTTC
* * *
47385 AAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAAAAATCTTAAAGGTTTTATCAA
1 AAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATC-TCAATG-TTTATCAA
* *
47450 TTTTATTTCAAGTGAAAC
64 TTTTGTTTCAAGAGAAAC
47468 AATTTCCAAA
Statistics
Matches: 257, Mismatches: 23, Indels: 24
0.85 0.08 0.08
Matches are distributed among these distances:
206 27 0.11
207 22 0.09
208 2 0.01
209 1 0.00
211 1 0.00
212 91 0.35
213 54 0.21
215 2 0.01
216 57 0.22
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (209 bp):
AAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAATCTCAATGTTTATCAATT
TTGTTTCAAGAGAAACTGCCTCAAGAGAGACAAAACTTGTCTCAAGAGAAACAATCTCAAAGGTT
TTATGTTTCAAGAGAAACTGTCTCAAGAGAAACAAAACTTTGTTTCAAGAGAAACAATCTCAAAG
TGTTTTTATGTTTC
Found at i:47622 original size:99 final size:101
Alignment explanation
Indices: 47448--47630 Score: 264
Period size: 99 Copynumber: 1.8 Consensus size: 101
47438 AGGTTTTATC
* * *
47448 AATTTTATTTCAAGTGAAACAATTTCCAAATTTTGTGTTTTGAAGAAAAATTGTTTCAAGTGAGA
1 AATTTTATTTCAAGTGAAACAATTTCCAAAATTTGTATTTTGAAGAAAAATTGTCTCAAGTGAGA
47513 CGAAATTTG-TTTTAAGAACAATCTCAAGTGAGATA
66 CGAAATTTGTTTTTAAGAACAATCTCAAGTGAGATA
* * * **
47548 AATTTTGTTTCAAGTGAAACAATTT-CAAAATTTGTATTTTTAGGGGAAATTGTCTCAAGTGAGA
1 AATTTTATTTCAAGTGAAACAATTTCCAAAATTTGTATTTTGAAGAAAAATTGTCTCAAGTGAGA
47612 TC-AAATTTGTTTTTAAGAA
66 -CGAAATTTGTTTTTAAGAA
47631 AAACAATCTC
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
99 39 0.53
100 34 0.47
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (101 bp):
AATTTTATTTCAAGTGAAACAATTTCCAAAATTTGTATTTTGAAGAAAAATTGTCTCAAGTGAGA
CGAAATTTGTTTTTAAGAACAATCTCAAGTGAGATA
Found at i:47641 original size:37 final size:37
Alignment explanation
Indices: 47600--47727 Score: 92
Period size: 37 Copynumber: 3.6 Consensus size: 37
47590 GGGGAAATTG
47600 TCTCAAGTGAGATCAAATTTGTTTTTAAGAAAAACAA
1 TCTCAAGTGAGATCAAATTTGTTTTTAAGAAAAACAA
* * * * **
47637 TCTC-A---A-AT---GTTTGTGTCTTAAGGAAGACTG
1 TCTCAAGTGAGATCAAATTTGT-TTTTAAGAAAAACAA
*
47667 TCTCAAGTGAGATGAAATTTGTTTTTAAGAAAAACAA
1 TCTCAAGTGAGATCAAATTTGTTTTTAAGAAAAACAA
* ** *
47704 TCTCAAATGTTATCAATTTTGTTT
1 TCTCAAGTGAGATCAAATTTGTTT
47728 CAAGGAAAAC
Statistics
Matches: 65, Mismatches: 17, Indels: 18
0.65 0.17 0.18
Matches are distributed among these distances:
29 5 0.08
30 14 0.22
31 1 0.02
32 2 0.03
33 1 0.02
34 1 0.02
35 2 0.03
36 1 0.02
37 33 0.51
38 5 0.08
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.38
Consensus pattern (37 bp):
TCTCAAGTGAGATCAAATTTGTTTTTAAGAAAAACAA
Found at i:52543 original size:4 final size:4
Alignment explanation
Indices: 52534--52558 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
52524 ATTAACATTA
52534 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
52559 CTCAATCACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:55306 original size:33 final size:33
Alignment explanation
Indices: 55202--55308 Score: 110
Period size: 33 Copynumber: 3.1 Consensus size: 33
55192 TTGAAACAAT
* *
55202 TATAATATATATATATATATATATATATATATATATA
1 TATAATATA-AGATATATATA-A-AT-TATATATTTA
*
55239 TATAATATAAGATATATATAAAATATATATTT-
1 TATAATATAAGATATATATAAATTATATATTTA
55271 TATTAATATAA-ACTATATATAAATTATATAGTTTA
1 TA-TAATATAAGA-TATATATAAATTATATA-TTTA
55306 TAT
1 TAT
55309 TTATATTATT
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
32 3 0.05
33 32 0.52
34 5 0.08
35 3 0.05
36 10 0.16
37 9 0.15
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (33 bp):
TATAATATAAGATATATATAAATTATATATTTA
Found at i:55328 original size:41 final size:41
Alignment explanation
Indices: 55264--55342 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
55254 ATATAAAATA
55264 TATATTTTATTAATATAAACTATATATAAAT-TATATAGTT
1 TATATTTTATTAATATAAACTATATATAAATATATATAGTT
* * *
55304 TATATTTATATTATTATATACTATATATAACTATATATA
1 TATATTT-TATTAATATAAACTATATATAAATATATATA
55343 TATTATGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 7 0.21
41 21 0.62
42 6 0.18
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (41 bp):
TATATTTTATTAATATAAACTATATATAAATATATATAGTT
Found at i:55392 original size:2 final size:2
Alignment explanation
Indices: 55202--55372 Score: 114
Period size: 2 Copynumber: 88.5 Consensus size: 2
55192 TTGAAACAAT
55202 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
55243 -A TA TA -A GA TA TA TA TA -A AA TA TA TA T- TT TA T- 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
* * * *
55279 TA AA CTA TA TA TA AA T- TA TA TA GTT TA TA TT TA TA T- TA T- TA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* *
55320 TA TA CTA TA TA TA -A CTA TA TA TA TA T- TA TG TA TA AA CTA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA
*
55361 TA GTT TA TA TA T
1 TA -TA TA TA TA T
55373 GAACTATTGA
Statistics
Matches: 134, Mismatches: 17, Indels: 36
0.72 0.09 0.19
Matches are distributed among these distances:
1 12 0.09
2 115 0.86
3 7 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:55435 original size:20 final size:20
Alignment explanation
Indices: 55202--55443 Score: 128
Period size: 20 Copynumber: 12.2 Consensus size: 20
55192 TTGAAACAAT
* *
55202 TATAATATATATATATATATA
1 TATAATTTATATATAAAT-TA
* * *
55223 TATATATATATATATATATAA
1 TATA-ATTTATATATAAATTA
** *
55244 TATAAGATATATATAAAATA
1 TATAATTTATATATAAATTA
55264 TAT-ATTT-TAT-T-AA-TA
1 TATAATTTATATATAAATTA
*
55279 TA-AA-CTATATATAAATTA
1 TATAATTTATATATAAATTA
* * *
55297 TATAGTTTATATTTATATTA
1 TATAATTTATATATAAATTA
* *
55317 T-T-ATATACTATATATAACTA
1 TATAATTTA-TATATA-AATTA
* *
55337 TATATATATTATGTATAAACTA
1 TATA-AT-TTATATATAAATTA
* * *
55359 TATAGTTTATATATGAACTA
1 TATAATTTATATATAAATTA
* *
55379 T-TGAA-CTATATATAAACTA
1 TAT-AATTTATATATAAATTA
*
55398 CATAATTTATTAATATAAATTA
1 TATAATTTA-T-ATATAAATTA
55420 TATAATTTATATATAAATTA
1 TATAATTTATATATAAATTA
55440 TATA
1 TATA
55444 TGAATTATAC
Statistics
Matches: 173, Mismatches: 29, Indels: 39
0.72 0.12 0.16
Matches are distributed among these distances:
14 1 0.01
15 8 0.05
16 3 0.02
17 3 0.02
18 10 0.06
19 24 0.14
20 62 0.36
21 13 0.08
22 40 0.23
23 7 0.04
24 2 0.01
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (20 bp):
TATAATTTATATATAAATTA
Found at i:55450 original size:11 final size:11
Alignment explanation
Indices: 55199--55452 Score: 81
Period size: 11 Copynumber: 23.6 Consensus size: 11
55189 AAATTGAAAC
55199 AATTATAATATA
1 AATTAT-ATATA
*
55211 TATATATATATA
1 AAT-TATATATA
*
55223 TATATATATATA
1 AAT-TATATATA
*
55235 TATATATAATATA
1 AAT-TAT-ATATA
55248 AGA-TATATATA
1 A-ATTATATATA
* *
55259 AAATATATATTT
1 AATTATATA-TA
*
55271 TATTA-ATATA
1 AATTATATATA
*
55281 AACTATATATA
1 AATTATATATA
55292 AATTATATAGT-
1 AATTATATA-TA
*
55303 --TTATATTTA
1 AATTATATATA
*
55312 TATTAT-TATA
1 AATTATATATA
* *
55322 TACTATATAT-
1 AATTATATATA
*
55332 AACTATATATA
1 AATTATATATA
* *
55343 TATTATGTATA
1 AATTATATATA
*
55354 AACTATATAGT-
1 AATTATATA-TA
*
55365 --TTATATATG
1 AATTATATATA
* *
55374 AA--CTAT-TG
1 AATTATATATA
*
55382 AACTATATATA
1 AATTATATATA
* * *
55393 AACTACATAATT
1 AATTATAT-ATA
*
55405 TATTA-ATATA
1 AATTATATATA
55415 AA-T-TATATA
1 AATTATATATA
*
55424 ATTTATATATA
1 AATTATATATA
*
55435 AATTATATATG
1 AATTATATATA
55446 AATTATA
1 AATTATA
55453 CAACTTATAC
Statistics
Matches: 187, Mismatches: 32, Indels: 47
0.70 0.12 0.18
Matches are distributed among these distances:
8 6 0.03
9 22 0.12
10 29 0.16
11 81 0.43
12 40 0.21
13 8 0.04
14 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (11 bp):
AATTATATATA
Found at i:55550 original size:3 final size:3
Alignment explanation
Indices: 55542--55606 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
55532 ATGTTTTAAT
* * *
55542 TTA TTA TTA TTA TTG TCA TTT TTA -TA TTA TT- TATA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA TTA TTA
55587 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
55607 TAATATGTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 3 0.06
3 46 0.88
4 2 0.04
5 1 0.02
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Done.