Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006487.1 Hibiscus syriacus cultivar Beakdansim tig00015769_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: 142685
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:339 original size:22 final size:22
Alignment explanation
Indices: 314--360 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
304 ATGAAGAACT
*
314 ACCTGTAAAATAAGAA-CACTAA
1 ACCTATAAAATAAGAATC-CTAA
*
336 ACCTATGAAATAAGAATCCTAA
1 ACCTATAAAATAAGAATCCTAA
358 ACC
1 ACC
361 AAAGAAAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.51, C:0.21, G:0.09, T:0.19
Consensus pattern (22 bp):
ACCTATAAAATAAGAATCCTAA
Found at i:367 original size:22 final size:22
Alignment explanation
Indices: 321--367 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
311 ACTACCTGTA
* *
321 AAATAAGAACACTAAACCTATG
1 AAATAAGAACACTAAACCAAAG
343 AAATAAGAATC-CTAAACCAAAG
1 AAATAAGAA-CACTAAACCAAAG
365 AAA
1 AAA
368 GACCCTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.60, C:0.17, G:0.09, T:0.15
Consensus pattern (22 bp):
AAATAAGAACACTAAACCAAAG
Found at i:1016 original size:22 final size:23
Alignment explanation
Indices: 991--1035 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
981 AAGATATTCA
*
991 CAATGGCAATTGGTAA-TATCAT
1 CAATGACAATTGGTAATTATCAT
1013 CAATGACAATTGGTAATTATCAT
1 CAATGACAATTGGTAATTATCAT
1036 GATTCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (23 bp):
CAATGACAATTGGTAATTATCAT
Found at i:4860 original size:22 final size:22
Alignment explanation
Indices: 4818--4860 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4808 GTTATTAAGA
* *
4818 TTCAAGGATGTGTGTATTTATT
1 TTCAAGGATGTGTGAACTTATT
4840 TTCAAGGAT-TGCTGAACTTAT
1 TTCAAGGATGTG-TGAACTTAT
4861 GCTTGTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (22 bp):
TTCAAGGATGTGTGAACTTATT
Found at i:7839 original size:3 final size:3
Alignment explanation
Indices: 7831--7894 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
7821 AAAAAATATG
* **
7831 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7875 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
7895 CGATAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:7869 original size:32 final size:32
Alignment explanation
Indices: 7833--7900 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
7823 AAAATATGTA
*
7833 ATAATAAATAATAATAA-AATAATAAGATAACG
1 ATAAT-AATAATAATAATAATAATAAAATAACG
7865 ATAATAATAATAATAATAATAATAAAATAACG
1 ATAATAATAATAATAATAATAATAAAATAACG
7897 ATAA
1 ATAA
7901 AAAAAACCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 11 0.32
32 23 0.68
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.26
Consensus pattern (32 bp):
ATAATAATAATAATAATAATAATAAAATAACG
Found at i:8335 original size:130 final size:130
Alignment explanation
Indices: 8105--8403 Score: 474
Period size: 130 Copynumber: 2.3 Consensus size: 130
8095 GTGACATGGT
* * ** * *
8105 TCCTACGTGATGAGGAAATCTGGTCAAGGGTTGACACTGCTCATACGTGATGAAGAGTTCTTGGC
1 TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGGC
*
8170 CATCTTAAGGTGATAACACGGTTCCTACATAATGAGGACGGCTGGTTATCTACGGTTGACACAGC
66 CATCTAAAGGTGATAACACGGTTCCTACATAATGAGGACGGCTGGTTATCTACGGTTGACACAGC
8235 TCCTACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAGAGTTC-TGG
1 TCCTACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTTGG
* * * *
8299 CCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGG
65 CCATCTAAAGGTGATAACACGGTTCCTACATAATGAGGACGGCTGGTTATCTACGGTTGACACAG
8364 C
130 C
*
8365 TCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGG
1 TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGG
8404 TTCCTACATA
Statistics
Matches: 156, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
129 9 0.06
130 119 0.76
131 28 0.18
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (130 bp):
TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGGC
CATCTAAAGGTGATAACACGGTTCCTACATAATGAGGACGGCTGGTTATCTACGGTTGACACAGC
Found at i:8351 original size:46 final size:45
Alignment explanation
Indices: 8138--8388 Score: 128
Period size: 43 Copynumber: 5.7 Consensus size: 45
8128 TCAAGGGTTG
* * ** **
8138 ACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGAGC-TGGTTATC-TAAGGTGATA
* * * * * *
8185 ACACGGTTCCTACATAATGAGGACG-GCTGGTTATCTACGGT--TG
1 ACACGGCTCCTACGTGATGAAGA-GAGCTGGTTATCTAAGGTGATA
* * * *
8228 ACACAGCTCCTACGTGATGAAGAGATCTGG---TCT--GGGGAATG
1 ACACGGCTCCTACGTGATGAAGAGAGCTGGTTATCTAAGGTG-ATA
* ** **
8269 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGAGCTGGTTATCT-AAGGTGATA
* * * *
8315 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCCTACGTGATGAAGA-GAGCTGGTTATCTAAGGTGATA
* *
8358 ACACGGCTCATACGTGATGAAGAGATCTGGT
1 ACACGGCTCCTACGTGATGAAGAGAGCTGGT
8389 CTGGGGATGA
Statistics
Matches: 156, Mismatches: 35, Indels: 30
0.71 0.16 0.14
Matches are distributed among these distances:
38 2 0.01
40 3 0.02
41 29 0.19
42 2 0.01
43 49 0.31
44 3 0.02
45 9 0.06
46 36 0.23
47 22 0.14
48 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (45 bp):
ACACGGCTCCTACGTGATGAAGAGAGCTGGTTATCTAAGGTGATA
Found at i:8387 original size:89 final size:83
Alignment explanation
Indices: 8267--8427 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
8257 GTCTGGGGAA
* * * *
8267 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGATAACACGGTTCCTACATAA
8332 TGAGGACGGCTGGTTATCTATGGT
60 TGAGGACGGCTGGTTATCTATGGT
*
8356 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATAATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATAATGAGGA
8421 CGGCTGG
66 CGGCTGG
8428 CCATCTTTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 33 0.49
86 3 0.04
89 31 0.46
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (83 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATAATGAGGA
CGGCTGGTTATCTATGGT
Found at i:8501 original size:28 final size:28
Alignment explanation
Indices: 8470--8527 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
8460 CAAATTAAAT
8470 ATTTGTTTCAA-AAGAAACAAACCCAAAG
1 ATTTGTTTCAAGAA-AAACAAACCCAAAG
* *
8498 ATTTGTTTCAAGAAAAATAAACTCAAAG
1 ATTTGTTTCAAGAAAAACAAACCCAAAG
8526 AT
1 AT
8528 GATATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (28 bp):
ATTTGTTTCAAGAAAAACAAACCCAAAG
Found at i:8593 original size:65 final size:64
Alignment explanation
Indices: 8534--8658 Score: 162
Period size: 64 Copynumber: 2.0 Consensus size: 64
8524 AGATGATATT
* * *
8534 TTTAAA-AGCAACTGTCTCAAAAAAGACCAAATTCGTTTTAAGGGAAACGACTCAAAGATGACG
1 TTTAAAGAGAAACTGTCTCAAAAAAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGATGACG
* ** **
8597 TTTAAAGGGAAACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAATTGATCTCAAAGATG
1 TTTAAAGAGAAACTGTCTCAAAAAAGACAAAATTCGTTTAAAGGGAAACGA-CTCAAAGATG
8659 TTTGTTTTGT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 6 0.12
64 36 0.69
65 10 0.19
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (64 bp):
TTTAAAGAGAAACTGTCTCAAAAAAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGATGACG
Found at i:8887 original size:15 final size:15
Alignment explanation
Indices: 8863--8921 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
8853 AAGATGATCT
*
8863 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
8878 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
8893 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
8908 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
8922 CGACTCAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:9149 original size:62 final size:63
Alignment explanation
Indices: 9078--9201 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
9068 AATGTGGGTA
* *
9078 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTATTT-CAAAGGAAACAAACTCAAAGATT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTATTTCCAAA-GAAACAAACTCAAAGATT
* * * * *
9140 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCCAAAGAAAGAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAAAGAT
9202 GGATTACATC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
62 17 0.32
63 32 0.60
64 4 0.08
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAAAGATT
Found at i:9347 original size:30 final size:28
Alignment explanation
Indices: 9296--9352 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
9286 GACAACATTC
* * *
9296 ATTTTTTAAAGAAATAGACTCACAGATG
1 ATTTTTTAAAGAAACAAACTCAAAGATG
9324 ATTTTGTTAAGAGAAACAAACTCAAAGAT
1 ATTTT-TTAA-AGAAACAAACTCAAAGAT
9353 TTTCAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 4 0.17
30 15 0.62
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (28 bp):
ATTTTTTAAAGAAACAAACTCAAAGATG
Found at i:9481 original size:37 final size:37
Alignment explanation
Indices: 9435--9561 Score: 112
Period size: 37 Copynumber: 3.6 Consensus size: 37
9425 GAAACAGATT
*
9435 CAAAGATTTTTTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGATTTTGTTTCAAAAGAAA-TATCTTAAGAGAGA
* **
9473 CAAA-ATTTTGTTTCCAAAG-AA-A-C---A-A-ACT
1 CAAAGATTTTGTTTCAAAAGAAATATCTTAAGAGAGA
9501 CAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
1 CAAAGA-TTTTGTTTCAAAAGAAA-TATCTTAAGAGAGA
*
9540 CAAA-ATTTTGTTTCCAAAGAAA
1 CAAAGATTTTGTTTCAAAAGAAA
9562 CAAACTCAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 23
0.69 0.08 0.23
Matches are distributed among these distances:
28 5 0.07
29 2 0.03
30 14 0.20
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 30 0.43
38 6 0.09
39 5 0.07
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (37 bp):
CAAAGATTTTGTTTCAAAAGAAATATCTTAAGAGAGA
Found at i:9530 original size:67 final size:66
Alignment explanation
Indices: 9382--9579 Score: 276
Period size: 67 Copynumber: 3.0 Consensus size: 66
9372 AAGGATTTAC
* * * * * * *
9382 TTCAAAAGAGACTGTCTCAAGAGATACAAAATTCAT-TTT--AAGAGAAACAGATTCAAAGATTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCCAA-AGAAACAAACTCAAAGATTT
9444 TTT
64 TTT
*
9447 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
9512 GT
66 -T
9514 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
9579 T
66 T
9580 GAAAAGAAAC
Statistics
Matches: 120, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.01
65 31 0.26
66 21 0.17
67 67 0.56
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (66 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
T
Found at i:9585 original size:27 final size:27
Alignment explanation
Indices: 9555--9606 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
9545 TTTTGTTTCC
9555 AAAGAAACAAACTCAAAGATTTTTTGA
1 AAAGAAACAAACTCAAAGATTTTTTGA
*
9582 AAAGAAACAATCTCAAAGATTTTTT
1 AAAGAAACAAACTCAAAGATTTTTT
9607 TTCACAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (27 bp):
AAAGAAACAAACTCAAAGATTTTTTGA
Found at i:9740 original size:25 final size:27
Alignment explanation
Indices: 9694--9787 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 27
9684 AAAACTTTGT
* *
9694 TTCAAAATAAATAGACTCAAAGATTT-
1 TTCAAAAGAAACAGACTCAAAGATTTA
9720 TTCAAAAGAAACA-ACTCAAAGATTTTTA
1 TTCAAAAGAAACAGACTCAAAGA--TTTA
*
9748 TTCAAAAGGAACAGACTCAAAGATTTA
1 TTCAAAAGAAACAGACTCAAAGATTTA
*
9775 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
9788 TGTCTCCAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.16
26 11 0.19
27 8 0.14
28 21 0.36
29 9 0.16
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (27 bp):
TTCAAAAGAAACAGACTCAAAGATTTA
Found at i:10116 original size:36 final size:36
Alignment explanation
Indices: 10032--10135 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
10022 GAGAAAATGA
* * *
10032 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAGTTTGTTTTTAGAGAAAT
* **
10066 AGTCTCAAATGAGACAAAGTTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAGTTTGTTTTTAGAGAAAT
10102 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAGTTTGTTTTTAGAGAAA
10136 ACGATCTCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 19 0.32
35 10 0.17
36 30 0.51
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAGTTTGTTTTTAGAGAAAT
Found at i:10163 original size:36 final size:36
Alignment explanation
Indices: 10033--10151 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
10023 AGAAAATGAT
* * * *
10033 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAGTTTGTTTTTAGAGA-AAAC
* **
10067 GTCTCAAATGAGACAAAGTTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAGTTTGTTTTTAGAGAAAAC
*
10103 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAGTTTGTTTTTAGAGAAAAC
10138 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
10152 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 19 0.27
35 12 0.17
36 39 0.56
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAGTTTGTTTTTAGAGAAAAC
Found at i:10165 original size:70 final size:69
Alignment explanation
Indices: 10032--10163 Score: 151
Period size: 70 Copynumber: 1.9 Consensus size: 69
10022 GAGAAAATGA
* *
10032 TGTCTCAAGCGAGACAAAATTTGCTTTAAGATATAGTCTCAAATGAGACAAAGTTTGTTTTTAGA
1 TGTCTCAAGCGAGACAAAATTTGCTTTAAGATAAAGTCTCAAATGAGACAAACTTTG-TTTTAGA
10097 GAAAT
65 GAAAT
* * * *
10102 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGA-AAACGATCTCAAGTGAGATC-AACTTTGTTT
1 TGTCTCAAGCGAGACAAAATTTG-CTTTAAGATAAA-G-TCTCAAATGAGA-CAAACTTTGTTT
10164 AGTGTGAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
70 24 0.46
71 10 0.19
72 17 0.33
73 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (69 bp):
TGTCTCAAGCGAGACAAAATTTGCTTTAAGATAAAGTCTCAAATGAGACAAACTTTGTTTTAGAG
AAAT
Found at i:10282 original size:105 final size:104
Alignment explanation
Indices: 10103--10342 Score: 301
Period size: 105 Copynumber: 2.3 Consensus size: 104
10093 TAGAGAAATT
* *
10103 GTCTCAAGCGAGAC-AAAGTTTGTTTT-TGAG-AAAACGATCTCAAGTGAGATCAACTTTGTTTA
1 GTCTCAAGCGAGACGAAA-TTTGTTTTAAGAGAAAAACAATCTCAAGTGAGATCAACTTTGTTTA
* * *
10165 GTGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
65 GAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* * *
10205 GTCTCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
10269 TA-AGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
63 TAGAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
10310 GTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAA
1 GTCTCAAGCGAGACGAAATTTGTTTTAAGAGAA
10343 TTTGTCTCAA
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
102 22 0.18
103 5 0.04
104 4 0.03
105 84 0.71
106 4 0.03
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (104 bp):
GTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAAAACAATCTCAAGTGAGATCAACTTTGTTTAG
AGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:10349 original size:36 final size:36
Alignment explanation
Indices: 10309--10445 Score: 170
Period size: 36 Copynumber: 3.8 Consensus size: 36
10299 AAAGGAAAAA
* * *
10309 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
* * **
10345 TGTCTCAAACGAGACAAAATTTGTTTTTAGA-AAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
*
10380 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-TTTTAAGAGAAAT
10416 TGTCTCAAGCGAGACAAAAATTTGTTTTAA
1 TGTCTCAAGCGAGAC-AAAATTTGTTTTAA
10446 AATTCTCAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
35 25 0.29
36 53 0.62
37 8 0.09
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:10419 original size:71 final size:72
Alignment explanation
Indices: 10309--10443 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 72
10299 AAAGGAAAAA
* * * *
10309 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATTTGTCTCAAACGAGAC-AAAATTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
10373 AGAAAGC
66 AGAAAGC
*
10380 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAATTGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTG-TTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTT
10444 AAAATTCTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 40 0.70
72 17 0.30
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (72 bp):
TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
AGAAAGC
Found at i:10823 original size:16 final size:16
Alignment explanation
Indices: 10802--10877 Score: 60
Period size: 16 Copynumber: 5.2 Consensus size: 16
10792 TGTAACATGC
10802 ATGTATGTGTTGATGT
1 ATGTATGTGTTGATGT
*
10818 ATGTA--T-AT-ATGT
1 ATGTATGTGTTGATGT
*
10830 ATGTATGAGTTGATGT
1 ATGTATGTGTTGATGT
*
10846 ATGTA--T-AT-ATGT
1 ATGTATGTGTTGATGT
*
10858 ATGTATGAGTTGATGT
1 ATGTATGTGTTGATGT
10874 ATGT
1 ATGT
10878 TTCTCAATCT
Statistics
Matches: 45, Mismatches: 7, Indels: 16
0.66 0.10 0.24
Matches are distributed among these distances:
12 18 0.40
13 2 0.04
14 1 0.02
15 2 0.04
16 22 0.49
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
ATGTATGTGTTGATGT
Found at i:10834 original size:28 final size:28
Alignment explanation
Indices: 10802--10877 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
10792 TGTAACATGC
*
10802 ATGTATGTGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
10830 ATGTATGAGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
10858 ATGTATGAGTTGATGTATGT
1 ATGTATGAGTTGATGTATGT
10878 TTCTCAATCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.47
Consensus pattern (28 bp):
ATGTATGAGTTGATGTATGTATATATGT
Found at i:10877 original size:4 final size:4
Alignment explanation
Indices: 10814--10864 Score: 56
Period size: 4 Copynumber: 13.8 Consensus size: 4
10804 GTATGTGTTG
* *
10814 ATGT ATGT ATAT ATGT ATGT ATG- A-GT -TG- ATGT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
10858 ATGT ATG
1 ATGT ATG
10865 AGTTGATGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 1 0.03
3 4 0.10
4 34 0.87
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:12078 original size:12 final size:11
Alignment explanation
Indices: 12050--12091 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
12040 CCTCTTTTTG
*
12050 TTCTTTGCTTT
1 TTCTTTGATTT
12061 TTCTTTGATTT
1 TTCTTTGATTT
12072 TTGCTTTGATTT
1 TT-CTTTGATTT
12084 TCTCTTTG
1 T-TCTTTG
12092 CTCTTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 12 0.43
12 15 0.54
13 1 0.04
ACGTcount: A:0.05, C:0.14, G:0.12, T:0.69
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:12103 original size:19 final size:19
Alignment explanation
Indices: 12075--12116 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
12065 TTGATTTTTG
12075 CTTTGATTTTCTCTTTGCT
1 CTTTGATTTTCTCTTTGCT
* *
12094 CTTTGTTTTTTTCTTTGCT
1 CTTTGATTTTCTCTTTGCT
12113 CTTT
1 CTTT
12117 TCTCTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.02, C:0.19, G:0.10, T:0.69
Consensus pattern (19 bp):
CTTTGATTTTCTCTTTGCT
Found at i:12108 original size:12 final size:13
Alignment explanation
Indices: 12093--12143 Score: 61
Period size: 12 Copynumber: 4.0 Consensus size: 13
12083 TTCTCTTTGC
12093 TCTTTG-TTTTTT
1 TCTTTGATTTTTT
* *
12105 TCTTTGCTCTTTTC
1 TCTTTGAT-TTTTT
12119 TCTTTGATTTTTT
1 TCTTTGATTTTTT
12132 TCTTTG-TTTTTT
1 TCTTTGATTTTTT
12144 ATTGGATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 12 0.35
13 11 0.32
14 11 0.32
ACGTcount: A:0.02, C:0.14, G:0.08, T:0.76
Consensus pattern (13 bp):
TCTTTGATTTTTT
Found at i:12115 original size:26 final size:27
Alignment explanation
Indices: 12085--12137 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
12075 CTTTGATTTT
12085 CTCTTTGCTCTTTG-TTTTTTTCTTTG
1 CTCTTTGCTCTTTGATTTTTTTCTTTG
*
12111 CTCTTTTCTCTTTGATTTTTTTCTTTG
1 CTCTTTGCTCTTTGATTTTTTTCTTTG
12138 TTTTTTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.02, C:0.19, G:0.09, T:0.70
Consensus pattern (27 bp):
CTCTTTGCTCTTTGATTTTTTTCTTTG
Found at i:14238 original size:31 final size:32
Alignment explanation
Indices: 14182--14243 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
14172 TGACAAAATG
14182 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
14214 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
14244 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:18114 original size:3 final size:3
Alignment explanation
Indices: 18108--18160 Score: 56
Period size: 3 Copynumber: 18.0 Consensus size: 3
18098 AAAAAATATG
* **
18108 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18152 TAA TAA TAA
1 TAA TAA TAA
18161 AAAAATAACG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 35 0.85
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:22711 original size:67 final size:67
Alignment explanation
Indices: 22597--22731 Score: 175
Period size: 67 Copynumber: 2.0 Consensus size: 67
22587 CAGAAAAAGA
* *
22597 TATTATTAAATATAGAGCGAGTTAAAACCAAATGAAAGTCTTTAATTTTTAAATTGAGACATAGG
1 TATTATCAAATATAGAGCGAGTTAAAACCAAATGAAAGTCTTTAATTTTCAAATTGAGACATAGG
22662 GG
66 GG
*** * *
22664 TATTATCAAATATAGAGCGAGTTAAATTTATAA-GAAAGT-TTTCAATTTTCGAATTGGGACATA
1 TATTATCAAATATAGAGCGAGTTAAAACCA-AATGAAAGTCTTT-AATTTTCAAATTGAGACATA
22727 GGGG
64 GGGG
22731 T
1 T
22732 GCAATAGTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 3 0.05
67 54 0.92
68 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.34
Consensus pattern (67 bp):
TATTATCAAATATAGAGCGAGTTAAAACCAAATGAAAGTCTTTAATTTTCAAATTGAGACATAGG
GG
Found at i:23264 original size:25 final size:26
Alignment explanation
Indices: 23218--23276 Score: 111
Period size: 25 Copynumber: 2.3 Consensus size: 26
23208 CTGATACAAC
23218 TTTAACTTAAATTTTTTTTTTTAAAA
1 TTTAACTTAAATTTTTTTTTTTAAAA
23244 TTTAACTTAAA-TTTTTTTTTTAAAA
1 TTTAACTTAAATTTTTTTTTTTAAAA
23269 TTTAACTT
1 TTTAACTT
23277 GACCAAGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 22 0.67
26 11 0.33
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTAACTTAAATTTTTTTTTTTAAAA
Found at i:23606 original size:204 final size:204
Alignment explanation
Indices: 23272--24033 Score: 1228
Period size: 204 Copynumber: 3.7 Consensus size: 204
23262 TTTAAAATTT
* * * *
23272 AACTTGACCAAGTCAGATTAGAACATGTCAGGTTCGAGTCTCATACCCATTCCAGGGTGCAAATG
1 AACTTGACCAAGTCAGATTAAAACCTGTCAGGTTCGAGTCTCATACCCATCCCAGGGTGCAAATA
* *
23337 GGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAACACGTGTTGTCGTTTC
66 GGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTGTTGCCGTTTC
23402 AGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTTAATTTTTAAA
131 AGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTTAATTTTTAAA
23467 AAAAAAATC
196 AAAAAAATC
* * *
23476 AACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATGCCCATCCCGGGGTGCAAATA
1 AACTTGACCAAGTCAGATTAAAACCTGTCAGGTTCGAGTCTCATACCCATCCCAGGGTGCAAATA
*
23541 GGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCTCAATACGTGTTGCCGTTTC
66 GGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTGTTGCCGTTTC
*
23606 AGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTAAACTTAATTTTTAAA
131 AGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTTAATTTTTAAA
23671 AAAAAAATC
196 AAAAAAATC
* *
23680 AACTTGACCAAGTCAGATTAAAACCTGTCAGGTTCGAGTCTCATGCCCATCCCAGAGTGCAAATA
1 AACTTGACCAAGTCAGATTAAAACCTGTCAGGTTCGAGTCTCATACCCATCCCAGGGTGCAAATA
* *
23745 GGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTTCCCATGTGCCCAATACGTGTTTCCGTTTC
66 GGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTGTTGCCGTTTC
* * *
23810 AGGATCAATGGTTTCATTTTTTCACCCTAAGCCGAACCCGATACGACTTGAACTTAAATTTTTTT
131 AGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTT-AA-TTTTTA
*
23875 TAAAAAAAATC
194 AAAAAAAAATC
* * * *
23886 AACTTGACCAAGTCAGATTAAAACCTATCAAGTTCGAGTCTCATACCCATCCC---GT--AGATG
1 AACTTGACCAAGTCAGATTAAAACCTGTCAGGTTCGAGTCTCATACCCATCCCAGGGTGCAAATA
* *
23946 GGATTTATGCATTTTGCCAGCTAAAACCCCCCATTTCACCATGTGCCCAATACGTGTTGCCGTTT
66 GGATTTGTGCATTTTGCCAGCTAAAACCCCCCA-TTCCCCATGTGCCCAATACGTGTTGCCGTTT
24011 CAGGACCAATGGTTTTCATTTTT
130 CAGGACCAATGG-TTTCATTTTT
24034 CTTTCTTTTT
Statistics
Matches: 524, Mismatches: 30, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
201 35 0.07
202 39 0.07
203 12 0.02
204 371 0.71
205 2 0.00
206 65 0.12
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (204 bp):
AACTTGACCAAGTCAGATTAAAACCTGTCAGGTTCGAGTCTCATACCCATCCCAGGGTGCAAATA
GGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTGTTGCCGTTTC
AGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTTAATTTTTAAA
AAAAAAATC
Found at i:25614 original size:29 final size:27
Alignment explanation
Indices: 25581--25754 Score: 76
Period size: 28 Copynumber: 6.2 Consensus size: 27
25571 TTTTAATCAA
25581 AATATTATTTATTTATTAATATTTATAAT
1 AATATTATTTATTTA-T-ATATTTATAAT
* *
25610 AATATAATATAATATTTTTAATATTTTATAA-
1 AATAT--TAT-TTATTTAT-ATA-TTTATAAT
* * *
25641 AATAATCAATTATATTATA-ATAATATAA-
1 AAT-ATTATTTAT-TTATATAT-TTATAAT
* *
25669 GATATTATATT-TTTAT-T-TTAATAAT
1 AATATTAT-TTATTTATATATTTATAAT
* *
25694 ATATAATATTTTTTTATATATTTAATAAT
1 A-ATATTATTTATTTATATATTT-ATAAT
*
25723 GAATAATA-TTATTTATATATTTA-AAT
1 -AATATTATTTATTTATATATTTATAAT
25749 AATATT
1 AATATT
25755 TTAATAAAGA
Statistics
Matches: 112, Mismatches: 17, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
24 4 0.04
25 8 0.07
26 18 0.16
27 7 0.06
28 25 0.22
29 20 0.18
30 5 0.04
31 11 0.10
32 14 0.12
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
AATATTATTTATTTATATATTTATAAT
Found at i:25707 original size:26 final size:29
Alignment explanation
Indices: 25650--25753 Score: 110
Period size: 29 Copynumber: 3.6 Consensus size: 29
25640 AAATAATCAA
*
25650 TTATATTATAATAATATA-AGATATTATATT
1 TTATATTTTAATAATATATA-ATATT-TATT
25680 TT-TATTTTAATAATATATAATATTT-TT
1 TTATATTTTAATAATATATAATATTTATT
25707 TTATATATTTAATAATGA-ATAATA-TTATT
1 TTATAT-TTTAATAAT-ATATAATATTTATT
*
25736 TATATATTTAAATAATAT
1 T-TATATTTTAATAATAT
25754 TTTAATAAAG
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
27 4 0.06
28 7 0.11
29 45 0.69
30 9 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
TTATATTTTAATAATATATAATATTTATT
Found at i:25711 original size:52 final size:51
Alignment explanation
Indices: 25602--25746 Score: 118
Period size: 52 Copynumber: 2.7 Consensus size: 51
25592 TTTATTAATA
*
25602 TTTATAATAATATAATATAATATTTTTAATATTTTATAAAATAATCAATTAT
1 TTTATAATAATATAATATAATATTTTTAATATTTAATAAAATAAT-AATTAT
* * *
25654 ATTATAATAATATAAGATATTATATTTTT-AT-TTTAATAATATATAAT-ATTTT
1 TTTATAATAATAT-A-ATATAATATTTTTAATATTTAATAA-A-ATAATAATTAT
*
25706 TTTAT-ATATTTAATAATGAATAATATTATTTATATATTTAA
1 TTTATAATA-AT-ATAAT--ATAATATT-TTTA-ATATTTAA
25747 ATAATATTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
51 5 0.07
52 29 0.39
53 13 0.18
54 20 0.27
56 2 0.03
57 5 0.07
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (51 bp):
TTTATAATAATATAATATAATATTTTTAATATTTAATAAAATAATAATTAT
Found at i:25731 original size:19 final size:19
Alignment explanation
Indices: 25709--25761 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
25699 ATATTTTTTT
*
25709 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
25728 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
25750 ATAT-TTTAATAA
1 ATATATTTAATAA
25762 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:25782 original size:23 final size:23
Alignment explanation
Indices: 25756--25800 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25746 AATAATATTT
25756 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
25779 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
25801 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:26137 original size:14 final size:14
Alignment explanation
Indices: 26103--26143 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
26093 AAATATAATT
*
26103 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
26117 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
* *
26131 CGTTTTCCAGAAA
1 CATTTTCCGGAAA
26144 TGTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:26166 original size:14 final size:15
Alignment explanation
Indices: 26145--26190 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
26135 TTCCAGAAAT
26145 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
26160 G-AATTCAAATTCTA
1 GTAATTCATTTTCCA
26174 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
26189 GT
1 GT
26191 TCCAGTAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:26170 original size:20 final size:20
Alignment explanation
Indices: 26133--26171 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
26123 CCGGAAAACG
**
26133 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
26153 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
26172 TAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:26202 original size:36 final size:35
Alignment explanation
Indices: 26155--26223 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
26145 GTAATTCATT
*
26155 TTCCAGAATTCAAATTCTAGTAATTCATTTTCCAG
1 TTCCAGAATTCAAATTCCAGTAATTCATTTTCCAG
*
26190 TTCCAGTAATTCAAATTCCAGTAATTTATTTTCC
1 TTCCAG-AATTCAAATTCCAGTAATTCATTTTCC
26224 GGAAAACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.42
Consensus pattern (35 bp):
TTCCAGAATTCAAATTCCAGTAATTCATTTTCCAG
Found at i:26581 original size:49 final size:49
Alignment explanation
Indices: 26509--26603 Score: 147
Period size: 49 Copynumber: 1.9 Consensus size: 49
26499 AGCGTGTGTT
*
26509 CAGGGGCGGACCTCCATGGTGCCCAAGGTATCCTAGGCAACCCCTCATC
1 CAGGGGCGGACCTCCATGGTGCCCAAGGTATCCCAGGCAACCCCTCATC
**
26558 CAGGGGCGGACCT-CAGTGGTGCCCGGGGTATCCCAGGCAACCCCTC
1 CAGGGGCGGACCTCCA-TGGTGCCCAAGGTATCCCAGGCAACCCCTC
26604 CACAAGTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
48 2 0.05
49 40 0.95
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.15
Consensus pattern (49 bp):
CAGGGGCGGACCTCCATGGTGCCCAAGGTATCCCAGGCAACCCCTCATC
Found at i:28191 original size:18 final size:20
Alignment explanation
Indices: 28163--28202 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
28153 AAAATATTCA
28163 ATTTAATATTATTTTA-TAT
1 ATTTAATATTATTTTATTAT
28182 ATTT-ATATTATTTTATTAT
1 ATTTAATATTATTTTATTAT
28201 AT
1 AT
28203 AAAATTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTAATATTATTTTATTAT
Found at i:29259 original size:20 final size:20
Alignment explanation
Indices: 29234--29303 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
29224 TTTATGCTGG
29234 TATCGATACTGACATTTTAA
1 TATCGATACTGACATTTTAA
*
29254 TATCGATACTGACATTTCAA
1 TATCGATACTGACATTTTAA
* ** *
29274 TATCGGTACTGACCCTTTAG
1 TATCGATACTGACATTTTAA
29294 TATCGATACT
1 TATCGATACT
29304 CACTATCTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (20 bp):
TATCGATACTGACATTTTAA
Found at i:29318 original size:40 final size:40
Alignment explanation
Indices: 29233--29323 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
29223 GTTTATGCTG
* * *
29233 GTATCGATACTGACATTTTAATATCGATACTGACATTTCA
1 GTATCGATACTGACACTTTAATATCGATACTCACATCTCA
* * * *
29273 ATATCGGTACTGACCCTTTAGTATCGATACTCACTATCT-A
1 GTATCGATACTGACACTTTAATATCGATACTCAC-ATCTCA
29313 GTATCGATACT
1 GTATCGATACT
29324 TCCAAGCTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
40 38 0.93
41 3 0.07
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (40 bp):
GTATCGATACTGACACTTTAATATCGATACTCACATCTCA
Found at i:37914 original size:69 final size:69
Alignment explanation
Indices: 37831--37967 Score: 274
Period size: 69 Copynumber: 2.0 Consensus size: 69
37821 GTCCCCATGA
37831 GGAGGTAGAAATTGAAGAATTAAGACAGATAATTTCATTGAGCTTGCAACTCGTCTCTCAGTCAT
1 GGAGGTAGAAATTGAAGAATTAAGACAGATAATTTCATTGAGCTTGCAACTCGTCTCTCAGTCAT
37896 ACTG
66 ACTG
37900 GGAGGTAGAAATTGAAGAATTAAGACAGATAATTTCATTGAGCTTGCAACTCGTCTCTCAGTCAT
1 GGAGGTAGAAATTGAAGAATTAAGACAGATAATTTCATTGAGCTTGCAACTCGTCTCTCAGTCAT
37965 ACT
66 ACT
37968 CGAGAAGTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (69 bp):
GGAGGTAGAAATTGAAGAATTAAGACAGATAATTTCATTGAGCTTGCAACTCGTCTCTCAGTCAT
ACTG
Found at i:42735 original size:30 final size:31
Alignment explanation
Indices: 42699--42767 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
42689 ACTTTTAAAA
42699 TTGCAATACAGT-CC-CAACCAGTTAGTTCGT
1 TTGCAATACAGTCCCTCAA-CAGTTAGTTCGT
*
42729 TTGCAATACAGTCCCTCAACATTTAGTTCGT
1 TTGCAATACAGTCCCTCAACAGTTAGTTCGT
42760 TTGCAATA
1 TTGCAATA
42768 TGGTCCCCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 12 0.33
31 21 0.58
32 3 0.08
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (31 bp):
TTGCAATACAGTCCCTCAACAGTTAGTTCGT
Found at i:43538 original size:12 final size:13
Alignment explanation
Indices: 43502--43545 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
43492 GCCCCGATTA
43502 CCCGATTACCCGC
1 CCCGATTACCCGC
43515 CCCGATTACCCGC
1 CCCGATTACCCGC
*
43528 CCCGA-TACCCGA
1 CCCGATTACCCGC
43540 CCCGAT
1 CCCGAT
43546 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:43677 original size:24 final size:24
Alignment explanation
Indices: 43645--43699 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
43635 ATATATATAT
* * *
43645 ATACCCGACCCGATTCTCGGCCCA
1 ATACCCGACCCAATACCCGGCCCA
*
43669 ATACCCGACCCAATACCCGGCCTA
1 ATACCCGACCCAATACCCGGCCCA
43693 ATACCCG
1 ATACCCG
43700 TTTAAATAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.45, G:0.15, T:0.15
Consensus pattern (24 bp):
ATACCCGACCCAATACCCGGCCCA
Found at i:43682 original size:12 final size:12
Alignment explanation
Indices: 43645--43699 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
43635 ATATATATAT
*
43645 ATACCCGACCCG
1 ATACCCGACCCA
* * *
43657 ATTCTCGGCCCA
1 ATACCCGACCCA
43669 ATACCCGACCCA
1 ATACCCGACCCA
* *
43681 ATACCCGGCCTA
1 ATACCCGACCCA
43693 ATACCCG
1 ATACCCG
43700 TTTAAATAAC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.25, C:0.45, G:0.15, T:0.15
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:60990 original size:48 final size:48
Alignment explanation
Indices: 60932--61094 Score: 281
Period size: 48 Copynumber: 3.4 Consensus size: 48
60922 CTTTCCTTAT
*
60932 TTTCAGCAAAGGATGCACCGTCAATTGGGTTGTTGGCTTGGCAACCAA
1 TTTCAACAAAGGATGCACCGTCAATTGGGTTGTTGGCTTGGCAACCAA
*
60980 TTTCAACAAAGGATGCACTGTCAATTGGGTTGTTGGCTTGGCAACCAA
1 TTTCAACAAAGGATGCACCGTCAATTGGGTTGTTGGCTTGGCAACCAA
* *
61028 TTTCAACAAATGATGCACCGTCAATTGGTTTGTTGGCTTGGCAACCAA
1 TTTCAACAAAGGATGCACCGTCAATTGGGTTGTTGGCTTGGCAACCAA
*
61076 TTTCAATAAAGGATGCACC
1 TTTCAACAAAGGATGCACC
61095 TGCAAATTTG
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 108 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (48 bp):
TTTCAACAAAGGATGCACCGTCAATTGGGTTGTTGGCTTGGCAACCAA
Found at i:64168 original size:2 final size:2
Alignment explanation
Indices: 64128--64160 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
64118 TGGTTGATAG
64128 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 T
64161 GCATATATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65129 original size:42 final size:42
Alignment explanation
Indices: 65070--65169 Score: 182
Period size: 42 Copynumber: 2.4 Consensus size: 42
65060 CCAAACTCAT
*
65070 CACCCGCCCACTACCCGCGACGAGTATAACTTTTTAAATTTA
1 CACCCGCCCACTACCCGCGACGAGTACAACTTTTTAAATTTA
*
65112 CACCCGCCCACTACCCGCGACGGGTACAACTTTTTAAATTTA
1 CACCCGCCCACTACCCGCGACGAGTACAACTTTTTAAATTTA
65154 CACCCGCCCACTACCC
1 CACCCGCCCACTACCC
65170 ACTAAAGTTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.26, C:0.40, G:0.12, T:0.22
Consensus pattern (42 bp):
CACCCGCCCACTACCCGCGACGAGTACAACTTTTTAAATTTA
Found at i:67084 original size:23 final size:22
Alignment explanation
Indices: 67058--67113 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
67048 AAAGCATACA
67058 TAAAATTTAATTTTGAAAAAAAT
1 TAAAATTTAATTTTG-AAAAAAT
*
67081 T-AAATTTAAATTTTGAAAAGAT
1 TAAAATTT-AATTTTGAAAAAAT
67103 TGAAAATTTAA
1 T-AAAATTTAA
67114 GTACTAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 13 0.45
23 10 0.34
24 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (22 bp):
TAAAATTTAATTTTGAAAAAAT
Found at i:67447 original size:5 final size:5
Alignment explanation
Indices: 67434--67478 Score: 81
Period size: 5 Copynumber: 9.0 Consensus size: 5
67424 TCTAATTCAC
*
67434 TTTCC TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
67479 ATTTTTTATG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTCT
Found at i:67635 original size:17 final size:17
Alignment explanation
Indices: 67613--67651 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
67603 TTTGCTTCTT
67613 GTTGTGGGTTTTTTAAG
1 GTTGTGGGTTTTTTAAG
67630 GTTGTGGGTTTTTTAAG
1 GTTGTGGGTTTTTTAAG
67647 GTTGT
1 GTTGT
67652 TACATTATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.36, T:0.54
Consensus pattern (17 bp):
GTTGTGGGTTTTTTAAG
Found at i:73710 original size:15 final size:15
Alignment explanation
Indices: 73690--73721 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
73680 GACGCTTTTC
73690 CATGATGGAAATATG
1 CATGATGGAAATATG
73705 CATGATGGAAATATG
1 CATGATGGAAATATG
73720 CA
1 CA
73722 AAAAAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.09, G:0.25, T:0.25
Consensus pattern (15 bp):
CATGATGGAAATATG
Found at i:78385 original size:38 final size:39
Alignment explanation
Indices: 78299--78399 Score: 132
Period size: 39 Copynumber: 2.6 Consensus size: 39
78289 ATACTTAAAG
* ***
78299 TTTAGTTTTTGTTTTATTTTAGTATCTGTTGTTAAAAAT
1 TTTAGTTTTTGTTTCATTTTAGTATCTACCGTTAAAAAT
* *
78338 TTTAATTTTTATTTCATTTTAGTATCTACCGTT-AAAAT
1 TTTAGTTTTTGTTTCATTTTAGTATCTACCGTTAAAAAT
*
78376 TTTAGTTTTTGTTTCAATTTAGTA
1 TTTAGTTTTTGTTTCATTTTAGTA
78400 CCCGTTTCAA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 26 0.49
39 27 0.51
ACGTcount: A:0.25, C:0.06, G:0.10, T:0.59
Consensus pattern (39 bp):
TTTAGTTTTTGTTTCATTTTAGTATCTACCGTTAAAAAT
Found at i:79589 original size:60 final size:60
Alignment explanation
Indices: 79476--79600 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 60
79466 ATAATCAAAC
* * *
79476 GACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACTCTTTATAGTCG-GTG
1 GACCATTTTGTAACATTTAATAGTCAAGGGACTCAACAAAGCAACTCTCTATAGTCGAG-G
** *
79536 GACCATTTTGTAACATTTAATAGTCAAGGGACTCAATTAAGCATCATC-CTATAGTCGAGG
1 GACCATTTTGTAACATTTAATAGTCAAGGGACTCAACAAAGCAAC-TCTCTATAGTCGAGG
79596 GACCA
1 GACCA
79601 ATTGTGTACT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 54 0.95
61 3 0.05
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (60 bp):
GACCATTTTGTAACATTTAATAGTCAAGGGACTCAACAAAGCAACTCTCTATAGTCGAGG
Found at i:79980 original size:6 final size:7
Alignment explanation
Indices: 79953--79977 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
79943 ATAAAATGCG
79953 ATTTTAT
1 ATTTTAT
79960 ATTTTAT
1 ATTTTAT
79967 ATTTTAT
1 ATTTTAT
79974 ATTT
1 ATTT
79978 ATAATGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTAT
Found at i:82517 original size:2 final size:2
Alignment explanation
Indices: 82510--82543 Score: 50
Period size: 2 Copynumber: 16.0 Consensus size: 2
82500 CTTTTAAATG
82510 AT AT AT AT AT AT AT AT AT AT AT AT CAT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT -AT AT
82544 TAGATTGGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 26 0.87
3 4 0.13
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:85186 original size:29 final size:28
Alignment explanation
Indices: 85131--85208 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 28
85121 TTTAAATGGT
*
85131 CTTTC-AAAT-GTTATAAAATAGTTATTAA
1 CTTTCTAAATAGTTAT-AAA-AGTCATTAA
85159 CCTTTCTAAATAGTTATAAAAGTCATTAA
1 -CTTTCTAAATAGTTATAAAAGTCATTAA
* *
85188 ATTTCTTAAATAGTTACAAAA
1 CTTTC-TAAATAGTTATAAAA
85209 TGGTCTTCTA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
28 4 0.09
29 27 0.63
30 7 0.16
31 5 0.12
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.40
Consensus pattern (28 bp):
CTTTCTAAATAGTTATAAAAGTCATTAA
Found at i:85592 original size:2 final size:2
Alignment explanation
Indices: 85587--85612 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
85577 ACCTAATTGA
85587 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
85613 GAATTATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91146 original size:98 final size:98
Alignment explanation
Indices: 91020--91200 Score: 299
Period size: 98 Copynumber: 1.8 Consensus size: 98
91010 CTTTGGCTAC
*
91020 TTGCTTTATATTGTTTGTTTTTGCTTCCTTAAATTGTTCATTTGTTACAAAGAAAAAGAAAATCG
1 TTGCTTTATATTGTTTGTTTTTGATTCCTTAAATTGTTCATTTGTTACAAAGAAAAAGAAAATCG
91085 TAGAAATGAGGATAATTTATACTAGTTTCTTCT
66 TAGAAATGAGGATAATTTATACTAGTTTCTTCT
* * * ** *
91118 TTGCTTTATATTGTTTGTTTTTTATTCCTTAAGTTGTTCATTTGTTATAAAGCGAAAGCAAATCG
1 TTGCTTTATATTGTTTGTTTTTGATTCCTTAAATTGTTCATTTGTTACAAAGAAAAAGAAAATCG
91183 TAGAAATGAGGATAATTT
66 TAGAAATGAGGATAATTT
91201 GGACTAAAGA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
98 76 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (98 bp):
TTGCTTTATATTGTTTGTTTTTGATTCCTTAAATTGTTCATTTGTTACAAAGAAAAAGAAAATCG
TAGAAATGAGGATAATTTATACTAGTTTCTTCT
Found at i:92479 original size:29 final size:30
Alignment explanation
Indices: 92436--92492 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
92426 GAGTGGGAAC
92436 AAAAGATTATCCAAAATT-AACACAAAAACA
1 AAAAGATTATCCAAAATTAAAC-CAAAAACA
* *
92466 AAAAGATT-TTCAAATTTAAACCAAAAA
1 AAAAGATTATCCAAAATTAAACCAAAAA
92493 TAATCTACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.54
30 11 0.46
ACGTcount: A:0.61, C:0.14, G:0.04, T:0.21
Consensus pattern (30 bp):
AAAAGATTATCCAAAATTAAACCAAAAACA
Found at i:94702 original size:11 final size:11
Alignment explanation
Indices: 94669--94709 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
94659 ACATATTTTC
94669 TATATAAAATA
1 TATATAAAATA
* *
94680 CATAGAAAATA
1 TATATAAAATA
94691 TATATAAAATA
1 TATATAAAATA
94702 TATGATAA
1 TAT-ATAA
94710 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 21 0.84
12 4 0.16
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (11 bp):
TATATAAAATA
Found at i:116742 original size:191 final size:191
Alignment explanation
Indices: 116418--116800 Score: 757
Period size: 191 Copynumber: 2.0 Consensus size: 191
116408 AGCTATTTAA
*
116418 TACGATACGAATGAACAACCCGGTTTTCTTTACACACATGGCACGGGTGCGGATTTTTTACCAAC
1 TACGATACGAATGAACAACCCGGTTTTCTTTACACACACGGCACGGGTGCGGATTTTTTACCAAC
116483 CCCATTTTACAAGAAAGAAACCTTGAAAAGATAGCATTTTTGTTGCTATAATAAAAAGGGAGTAA
66 CCCATTTTACAAGAAAGAAACCTTGAAAAGATAGCATTTTTGTTGCTATAATAAAAAGGGAGTAA
116548 ATTACGCATTTTTTACCTAAACTATCGGTTTTGATTCGTTTTAGTACATAAACATCCAATT
131 ATTACGCATTTTTTACCTAAACTATCGGTTTTGATTCGTTTTAGTACATAAACATCCAATT
116609 TACGATACGAATGAACAACCCGGTTTTCTTTACACACACGGCACGGGTGCGGATTTTTTACCAAC
1 TACGATACGAATGAACAACCCGGTTTTCTTTACACACACGGCACGGGTGCGGATTTTTTACCAAC
116674 CCCATTTTACAAGAAAGAAACCTTGAAAAGATAGCATTTTTGTTGCTATAATAAAAAGGGAGTAA
66 CCCATTTTACAAGAAAGAAACCTTGAAAAGATAGCATTTTTGTTGCTATAATAAAAAGGGAGTAA
116739 ATTACGCATTTTTTACCTAAACTATCGGTTTTGATTCGTTTTAGTACATAAACATCCAATT
131 ATTACGCATTTTTTACCTAAACTATCGGTTTTGATTCGTTTTAGTACATAAACATCCAATT
116800 T
1 T
116801 TTTCAAAACC
Statistics
Matches: 191, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
191 191 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (191 bp):
TACGATACGAATGAACAACCCGGTTTTCTTTACACACACGGCACGGGTGCGGATTTTTTACCAAC
CCCATTTTACAAGAAAGAAACCTTGAAAAGATAGCATTTTTGTTGCTATAATAAAAAGGGAGTAA
ATTACGCATTTTTTACCTAAACTATCGGTTTTGATTCGTTTTAGTACATAAACATCCAATT
Found at i:120136 original size:20 final size:21
Alignment explanation
Indices: 120092--120135 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
120082 ATTGGAATTT
120092 AAATTAAACGTTTGATATAAA
1 AAATTAAACGTTTGATATAAA
*
120113 AAATTAAA-GTTTAGATATTAA
1 AAATTAAACGTTT-GATATAAA
120134 AA
1 AA
120136 TGGAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (21 bp):
AAATTAAACGTTTGATATAAA
Found at i:122933 original size:2 final size:2
Alignment explanation
Indices: 122926--122956 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
122916 ATGCATGCCC
122926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
122957 CAAACATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:127946 original size:32 final size:32
Alignment explanation
Indices: 127869--127968 Score: 88
Period size: 26 Copynumber: 3.3 Consensus size: 32
127859 ATATAATTTA
* *
127869 AAATTAAAAATAAATTTGAAAGTTTGAGTGATT
1 AAATTAAAAAT-AATTTGAAAGTTTAAGTAATT
** *
127902 AAATTAGGAATAATTTGAAAG-TTAATTAATT
1 AAATTAAAAATAATTTGAAAGTTTAAGTAATT
*
127933 AAATT-AAAA-AA--T-AAA-TTTAAGTATTT
1 AAATTAAAAATAATTTGAAAGTTTAAGTAATT
127959 AAATTAAAAA
1 AAATTAAAAA
127969 AATAAACTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
26 16 0.29
27 5 0.09
29 2 0.04
30 2 0.04
31 12 0.21
32 10 0.18
33 9 0.16
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (32 bp):
AAATTAAAAATAATTTGAAAGTTTAAGTAATT
Found at i:127952 original size:26 final size:28
Alignment explanation
Indices: 127923--127979 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
127913 AATTTGAAAG
*
127923 TTAATTAATTAAATT-AAAAAATAAA-T
1 TTAAGTAATTAAATTAAAAAAATAAACT
*
127949 TTAAGTATTTAAATTAAAAAAATAAACT
1 TTAAGTAATTAAATTAAAAAAATAAACT
127977 TTA
1 TTA
127980 GTGACCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 13 0.48
27 10 0.37
28 4 0.15
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (28 bp):
TTAAGTAATTAAATTAAAAAAATAAACT
Found at i:128689 original size:13 final size:12
Alignment explanation
Indices: 128663--128696 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
128653 ACCAGCAAAC
128663 AAAAGGAAAAGG
1 AAAAGGAAAAGG
*
128675 AAAAAGAAAAGGG
1 AAAAGGAAAA-GG
128688 AAAAGGAAA
1 AAAAGGAAA
128697 TACACCATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AAAAGGAAAAGG
Found at i:128690 original size:7 final size:6
Alignment explanation
Indices: 128663--128696 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
128653 ACCAGCAAAC
*
128663 AAAAGG AAAAGG AAAAAG AAAAGGG AAAAGG AAA
1 AAAAGG AAAAGG AAAAGG AAAA-GG AAAAGG AAA
128697 TACACCATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:129420 original size:2 final size:2
Alignment explanation
Indices: 129415--129449 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
129405 ATTTTTTACA
129415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
129450 ATAACTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:130976 original size:19 final size:21
Alignment explanation
Indices: 130942--130986 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
130932 GTTAAATCCC
130942 TATTTTATTGAATAAA-ATAA
1 TATTTTATTGAATAAATATAA
* *
130962 TATTTT-TTTAATAAATATAT
1 TATTTTATTGAATAAATATAA
130982 TATTT
1 TATTT
130987 CAGGTCGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTTTATTGAATAAATATAA
Found at i:136492 original size:28 final size:28
Alignment explanation
Indices: 136452--136521 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
136442 GTTCCTACCT
136452 ATGAATGGTCACATTTTTTTTAACAAAG
1 ATGAATGGTCACATTTTTTTTAACAAAG
136480 ATGAATGGTCACATTTTTTTTAACAAAG
1 ATGAATGGTCACATTTTTTTTAACAAAG
136508 ATGAATGGTCACAT
1 ATGAATGGTCACAT
136522 ATAGATGATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (28 bp):
ATGAATGGTCACATTTTTTTTAACAAAG
Found at i:136608 original size:35 final size:35
Alignment explanation
Indices: 136562--136692 Score: 235
Period size: 35 Copynumber: 3.7 Consensus size: 35
136552 ACCTTTCACA
* *
136562 TATCAATGACCCAAAGGGTATTATTTACGGCATGT
1 TATCAAGGACCCAAAGGGTATTATTTAAGGCATGT
*
136597 TATCAAGGACCCATAGGGTATTATTTAAGGCATGT
1 TATCAAGGACCCAAAGGGTATTATTTAAGGCATGT
136632 TATCAAGGACCCAAAGGGTATTATTTAAGGCATGT
1 TATCAAGGACCCAAAGGGTATTATTTAAGGCATGT
136667 TATCAAGGACCCAAAGGGTATTATTT
1 TATCAAGGACCCAAAGGGTATTATTT
136693 CGTCTCGTAC
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 92 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (35 bp):
TATCAAGGACCCAAAGGGTATTATTTAAGGCATGT
Found at i:138398 original size:29 final size:29
Alignment explanation
Indices: 138356--138422 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
138346 ACCAGCCTTA
* * *
138356 GAAAAATTGGGGATCATTTCGTAAGTTTT
1 GAAAAATTGGGGATAAATTCGTAAATTTT
* *
138385 GAAAAGTTTGGGATAAATTCGTAAATTTT
1 GAAAAATTGGGGATAAATTCGTAAATTTT
138414 GAAAAATTG
1 GAAAAATTG
138423 ATGAAGAATC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
GAAAAATTGGGGATAAATTCGTAAATTTT
Found at i:139748 original size:40 final size:40
Alignment explanation
Indices: 139693--139814 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
139683 TGCAGGTTTT
139693 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
139733 TAATACACTTCGGTGTATATGGTGGGCACAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
139773 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
139813 TA
1 TA
139815 GCACTACGGT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:140020 original size:49 final size:48
Alignment explanation
Indices: 139953--140081 Score: 179
Period size: 49 Copynumber: 2.7 Consensus size: 48
139943 TAATGGCAAA
* * *
139953 TATATGGGTAAAATAAGCTTACGAGCTTATGGAA-TTTAAATGGTAAG
1 TATATTGGAAAAATAAGCTTACGAGCTTATGGAATTTTAAACGGTAAG
140000 TATATTGGAAAAAAATAAGCTTACGAGCTTATGGAATTTTAAACGGTAAG
1 TATATTGG--AAAAATAAGCTTACGAGCTTATGGAATTTTAAACGGTAAG
* * *
140050 TATTTTGGTAAAATAAGCTTACAAGCTTATGG
1 TATATTGGAAAAATAAGCTTACGAGCTTATGG
140082 GATAAATCGT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
47 7 0.10
48 22 0.30
49 25 0.34
50 19 0.26
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.33
Consensus pattern (48 bp):
TATATTGGAAAAATAAGCTTACGAGCTTATGGAATTTTAAACGGTAAG
Found at i:140504 original size:30 final size:30
Alignment explanation
Indices: 140470--140528 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
140460 TTTCGGAAGT
* *
140470 ACTGTAGTAGTTACTGTAGTGTATCGATGC
1 ACTGTAGCAGTTACTGTAGCGTATCGATGC
*
140500 ACTGTAGCAGTTGCTGTAGCGTATCGATG
1 ACTGTAGCAGTTACTGTAGCGTATCGATG
140529 TATAATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (30 bp):
ACTGTAGCAGTTACTGTAGCGTATCGATGC
Done.