Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002539.1 Hibiscus syriacus cultivar Beakdansim tig00005155_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: 64715
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:3557 original size:36 final size:36
Alignment explanation
Indices: 3482--3556 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 36
3472 ATTTTCGGGA
*
3482 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
3518 TTTTGCTA-TTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
3553 TTTT
1 TTTT
3557 TTAGCTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 30 0.79
36 8 0.21
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:7415 original size:19 final size:21
Alignment explanation
Indices: 7391--7445 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
7381 GAATGCAATT
7391 AGTGCATCGATGCA-T-AAGA
1 AGTGCATCGATGCACTGAAGA
* *
7410 AGTGCATCGATACACTGTAGA
1 AGTGCATCGATGCACTGAAGA
7431 A-TGCATCGATGCACT
1 AGTGCATCGATGCACT
7446 TCAAGGGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.42
20 14 0.45
21 4 0.13
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (21 bp):
AGTGCATCGATGCACTGAAGA
Found at i:8179 original size:20 final size:22
Alignment explanation
Indices: 8154--8208 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
8144 AGGGTTCATA
8154 GGTCATTCGGGACA-T-ACAGT
1 GGTCATTCGGGACATTCACAGT
*
8174 GGTCATTCGGGACATTTCATAGT
1 GGTCATTCGGGACA-TTCACAGT
8197 GGTCATTCGGGA
1 GGTCATTCGGGA
8209 TAAATTCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 14 0.45
22 1 0.03
23 16 0.52
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (22 bp):
GGTCATTCGGGACATTCACAGT
Found at i:14565 original size:19 final size:19
Alignment explanation
Indices: 14534--14585 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
14524 ATGCATTGGG
14534 CTATGAA-CTTGAAAATAAA
1 CTATGAATC-TGAAAATAAA
* *
14553 CTATGAATCTGAAATTAAG
1 CTATGAATCTGAAAATAAA
* *
14572 TTATGAATCCGAAA
1 CTATGAATCTGAAA
14586 TGAGTTATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (19 bp):
CTATGAATCTGAAAATAAA
Found at i:14593 original size:18 final size:19
Alignment explanation
Indices: 14554--14595 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
14544 GAAAATAAAC
*
14554 TATGAATCTGAAATTAAGT
1 TATGAATCCGAAATTAAGT
*
14573 TATGAATCCGAAA-TGAGT
1 TATGAATCCGAAATTAAGT
14591 TATGA
1 TATGA
14596 GTTTGGAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.33
Consensus pattern (19 bp):
TATGAATCCGAAATTAAGT
Found at i:14699 original size:19 final size:19
Alignment explanation
Indices: 14652--14699 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
14642 AGTATGAATT
*
14652 ATGAAAATGAAAAGTGAAAG
1 ATGAAAATG-AAAGCGAAAG
**
14672 -TGATTATGAAAGCGAAAG
1 ATGAAAATGAAAGCGAAAG
14690 ATGAAAATGA
1 ATGAAAATGA
14700 GATATGAAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.19
Consensus pattern (19 bp):
ATGAAAATGAAAGCGAAAG
Found at i:17836 original size:29 final size:29
Alignment explanation
Indices: 17722--17866 Score: 166
Period size: 29 Copynumber: 5.0 Consensus size: 29
17712 AAATGTTAAC
* * *
17722 TTTTTCAAAATAATTCCCTGAATGTCACC
1 TTTTTCAAAATATTTCCCAGAATGTCACA
* *
17751 TTTTTCAAAATATTTCCTAGAATGTCACC
1 TTTTTCAAAATATTTCCCAGAATGTCACA
* *
17780 TTTTTAAAAATATTCCCCA-AAGTGTCACA
1 TTTTTCAAAATATTTCCCAGAA-TGTCACA
*
17809 TTTTTCAAAATATTTCCCAGAATATCACA
1 TTTTTCAAAATATTTCCCAGAATGTCACA
* * *
17838 TTGTTCACAAAAAATTCCCAGAATGTCAC
1 TTTTTCA-AAATATTTCCCAGAATGTCAC
17867 CGGGTCGGGT
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
28 2 0.02
29 77 0.78
30 20 0.20
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.36
Consensus pattern (29 bp):
TTTTTCAAAATATTTCCCAGAATGTCACA
Found at i:17920 original size:19 final size:19
Alignment explanation
Indices: 17896--17949 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
17886 GGTCGGGTCA
*
17896 GACCGGTCAACCCGGTTCG
1 GACCGGTCAAACCGGTTCG
* *
17915 GACCGGTCAAACCAGTTTG
1 GACCGGTCAAACCGGTTCG
*
17934 GACCGGTCAAGCCGGT
1 GACCGGTCAAACCGGT
17950 CAACCAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCG
Found at i:25160 original size:29 final size:29
Alignment explanation
Indices: 25119--25278 Score: 148
Period size: 29 Copynumber: 5.6 Consensus size: 29
25109 CACATTCGAA
* * *
25119 AATTTCCAAAATGTCAACTTTTTCAAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
25148 AATTCCCAGAATGTCACCTTTTT-AAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
* * * *
25176 ATTTCCTATAATGTCA-C-TTTTCAAAAC
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
* ** * * *
25203 ATTTCCTTGAGTGTCACCTTTATGAAAAT
1 AATTCCCAGAATGTCACCTTTTTCAAAAT
* *
25232 ATTTCCCAGAATATCACCTTTTTCACAAA-
1 AATTCCCAGAATGTCACCTTTTTCA-AAAT
25261 AATTCCCAGAATGTCACC
1 AATTCCCAGAATGTCACC
25279 GGGTCAGGTC
Statistics
Matches: 106, Mismatches: 21, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
26 4 0.04
27 18 0.17
28 19 0.18
29 62 0.58
30 3 0.03
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (29 bp):
AATTCCCAGAATGTCACCTTTTTCAAAAT
Found at i:25206 original size:27 final size:27
Alignment explanation
Indices: 25120--25237 Score: 94
Period size: 28 Copynumber: 4.2 Consensus size: 27
25110 ACATTCGAAA
25120 ATTTCC-AAAATGTCAACTTTTTCAAAAT
1 ATTTCCTAAAATGTC-AC-TTTTCAAAAT
* * * *
25148 AATTCCCAGAATGTCACCTTTTTAAAAT
1 ATTTCCTAAAATGTCA-CTTTTCAAAAT
* *
25176 ATTTCCTATAATGTCACTTTTCAAAAC
1 ATTTCCTAAAATGTCACTTTTCAAAAT
** * *
25203 ATTTCCTTGAGTGTCACCTTTATGAAAAT
1 ATTTCCTAAAATGTCA-CTTT-TCAAAAT
25232 ATTTCC
1 ATTTCC
25238 CAGAATATCA
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
27 22 0.30
28 32 0.44
29 19 0.26
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (27 bp):
ATTTCCTAAAATGTCACTTTTCAAAAT
Found at i:25299 original size:18 final size:18
Alignment explanation
Indices: 25273--25311 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
25263 TTCCCAGAAT
*
25273 GTCACCGGGTCAGGTCGG
1 GTCAACGGGTCAGGTCGG
*
25291 GTCAACGGGTCGGGTCGG
1 GTCAACGGGTCAGGTCGG
25309 GTC
1 GTC
25312 GGGTCAGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.46, T:0.18
Consensus pattern (18 bp):
GTCAACGGGTCAGGTCGG
Found at i:25446 original size:10 final size:11
Alignment explanation
Indices: 25419--25452 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
25409 CGCTTCCGGC
25419 CTCCAAAAATT
1 CTCCAAAAATT
*
25430 CTGCAAAAATT
1 CTCCAAAAATT
25441 -TCCAAAAATT
1 CTCCAAAAATT
25451 CT
1 CT
25453 TTTAAGCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.44, C:0.24, G:0.03, T:0.29
Consensus pattern (11 bp):
CTCCAAAAATT
Found at i:36996 original size:8 final size:8
Alignment explanation
Indices: 36983--37035 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
36973 GGGGCCTATA
36983 AAAATAAT
1 AAAATAAT
36991 AAAATAAT
1 AAAATAAT
36999 AATAATAAT
1 AA-AATAAT
*
37008 AATA-AAT
1 AAAATAAT
37015 -AAATAAAT
1 AAAAT-AAT
*
37023 AATATAAT
1 AAAATAAT
37031 AAAAT
1 AAAAT
37036 GTTTTTGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 2 0.05
7 3 0.08
8 21 0.57
9 11 0.30
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATAAT
Found at i:36999 original size:3 final size:3
Alignment explanation
Indices: 36980--37032 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
36970 TGTGGGGCCT
*
36980 ATA AAA ATA ATA A-A ATA ATA ATA ATA ATA ATAA ATAA ATAA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A AT-A AT-A ATA ATA
37026 ATA ATA A
1 ATA ATA A
37033 AATGTTTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 30 0.67
4 11 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:37519 original size:84 final size:82
Alignment explanation
Indices: 37376--37892 Score: 524
Period size: 84 Copynumber: 6.2 Consensus size: 82
37366 CTGAATGGAA
* * * * * *
37376 TCGAACTCGAAGGTCTTTG--GTAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGGTG
1 TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGAT-GTG
* *
37439 CCTTTGAGCTGAGTGGAG
65 CCTTGGAGCTGAGTGTAG
* * * *
37457 TCGAACTCGAAGGTCTTTGTTGACAAATAACCCTTCTAGCCTTAAGTTATGCCGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTG-CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
*** *
37522 CCCTCAAAGCTGAGTGTAA
65 -CCTTGGAGCTGAGTGTAG
* * *
37541 TCGAACTC-AAGGGTCTTTG--GCAGATAGCCCTTCTCGACTTAGGTTATGCTGCAAATGATGTG
1 TCGAACTCGAA-GGTCTTTGTTGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
37603 CCTTGGAACTGAGAGTAG
65 CCTTGGAGCTGAGTGTAG
* * *
37621 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTAAGTTATGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTT-GTT-GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
*
37686 GCCTTGGAGCTGAGCGTAG
64 GCCTTGGAGCTGAGTGTAG
* * * * * *
37705 TCGAACTCGAAGGTCTTT-TGGTCACTGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATG
1 TCGAACTCGAAGGTCTTTGTTG-CA--GATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATG
* * *
37769 TGCCCTCGAAGCTGAGTGTAA
63 TG-CCTTGGAGCTGAGTGTAG
* * * * *
37790 TCGAACTCGAGGGTCTTCAGTTGGCAGATAACCCTTCTTGACTTAAGTTATGTTACAAATGATGT
1 TCGAACTCGAAGGTCTT-TGTT-GCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
37855 GCCTTGGAGCTGAGTGTAG
64 GCCTTGGAGCTGAGTGTAG
*
37874 TCGAACTCGAAGGCCTTTG
1 TCGAACTCGAAGGTCTTTG
37893 GTGGGCACGA
Statistics
Matches: 359, Mismatches: 60, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
80 27 0.08
81 58 0.16
82 4 0.01
83 7 0.02
84 195 0.54
85 64 0.18
87 3 0.01
88 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (82 bp):
TCGAACTCGAAGGTCTTTGTTGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
CTTGGAGCTGAGTGTAG
Found at i:37821 original size:169 final size:165
Alignment explanation
Indices: 37376--37894 Score: 609
Period size: 165 Copynumber: 3.1 Consensus size: 165
37366 CTGAATGGAA
* *
37376 TCGAACTCGAAGGTCTTTGGT-AGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGGTGC
1 TCGAACTCGAAGGTCTTTGGTCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGAT-GTGC
* * * * * *
37440 CTTTG-AGCTGAGTGGAGTCGAACTCGAAGGTCTTTGTTGACAAATAACCCTTCTAGCCTTAAGT
65 CTTCGAAGCTGAGTGTAGTCGAACTCGAAGGTCTTAGTTGGCAGATAACCCTTCTAGACTTAAGT
* * *** *
37504 TATGCCGTAAATGATGTGCCCTCAAAGCTGAGTGTAA
130 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGTGTAG
* *
37541 TCGAACTC-AAGGGTCTTTGG-CAGATAGCCCTTCTCGACTT-AGGTTATGCTGCAAATGATGTG
1 TCGAACTCGAA-GGTCTTTGGTCAGATAGCCCTTCTAGCCTTGA-GTTATGCTGCAAATGATGTG
* * * * *
37603 CCTTGGAA-CTGAGAGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTATCGACTTAA
64 CCTTCGAAGCTGAGTGTAGTCGAACTCGAAGGTC-TTAGTTGGCAGATAACCCTTCTAGACTTAA
* *
37667 GTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
128 GTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAG
* * * *
37705 TCGAACTCGAAGGTCTTTTGGTCACTGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGT
1 TCGAACTCGAAGGTC-TTTGGTCA--GATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT
* * * *
37770 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTCAGTTGGCAGATAACCCTTCTTGACTTA
63 GCCTTCGAAGCTGAGTGTAGTCGAACTCGAAGGTCTT-AGTTGGCAGATAACCCTTCTAGACTTA
* *
37835 AGTTATGTTACAAATGATGTGCCTTGGAGCTGAGTGTAG
127 AGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAG
*
37874 TCGAACTCGAAGGCCTTTGGT
1 TCGAACTCGAAGGTCTTTGGT
37895 GGGCACGATT
Statistics
Matches: 302, Mismatches: 39, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
164 59 0.20
165 99 0.33
166 2 0.01
168 46 0.15
169 96 0.32
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (165 bp):
TCGAACTCGAAGGTCTTTGGTCAGATAGCCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
TTCGAAGCTGAGTGTAGTCGAACTCGAAGGTCTTAGTTGGCAGATAACCCTTCTAGACTTAAGTT
ATGCTGCAAATGATGTGCCTTGGAGCTGAGTGTAG
Found at i:42230 original size:33 final size:36
Alignment explanation
Indices: 42153--42241 Score: 93
Period size: 33 Copynumber: 2.6 Consensus size: 36
42143 TAAACATAAG
*
42153 AAAAG-AATAATAAAAATATTAATATAATAATATTA
1 AAAAGAAATAATAAATATATTAATATAATAATATTA
* *
42188 ATAATAAATAATAAATATA-T-ATAT-ATAA-ATGTA
1 AAAAGAAATAATAAATATATTAATATAATAATAT-TA
42221 AAAAGAAATAA-AAA-ATATTAA
1 AAAAGAAATAATAAATATATTAA
42242 AATTAGGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
31 3 0.07
32 6 0.13
33 16 0.36
34 4 0.09
35 4 0.09
36 12 0.27
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.30
Consensus pattern (36 bp):
AAAAGAAATAATAAATATATTAATATAATAATATTA
Found at i:42612 original size:34 final size:34
Alignment explanation
Indices: 42574--42658 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 34
42564 TCCTACTTGG
* *
42574 ACTCAAAATGC-TTCGGTTTTAGTGTTTCAGTAGA
1 ACTCAAAATACGTT-GGTTTTAGTGTTTCAATAGA
42608 ACTC-AAATACGTTGGTTTTAGTGTTTCAATAGA
1 ACTCAAAATACGTTGGTTTTAGTGTTTCAATAGA
42641 ACTC-AAATACGTTGGTTT
1 ACTCAAAATACGTTGGTTT
42659 ATTTTCTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
33 42 0.88
34 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (34 bp):
ACTCAAAATACGTTGGTTTTAGTGTTTCAATAGA
Found at i:42629 original size:33 final size:33
Alignment explanation
Indices: 42588--42658 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
42578 AAAATGCTTC
*
42588 GGTTTTAGTGTTTCAGTAGAACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
42621 GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
42654 GGTTT
1 GGTTT
42659 ATTTTCTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.21, T:0.41
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
Found at i:42719 original size:3 final size:3
Alignment explanation
Indices: 42705--42773 Score: 97
Period size: 3 Copynumber: 22.7 Consensus size: 3
42695 GGCCTGCAAA
42705 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42752 AAAT AAAT ATAT AAT -AT AAT AA
1 -AAT -AAT A-AT AAT AAT AAT AA
42774 AATGTTTTTG
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.06
3 48 0.77
4 10 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:43080 original size:21 final size:21
Alignment explanation
Indices: 43029--43081 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
43019 ATTGTGACTA
43029 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
43050 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
43071 TCGCAATGCGA
1 TCGCAATGCGA
43082 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:43101 original size:41 final size:41
Alignment explanation
Indices: 43056--43145 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
43046 AATTTCGCGT
* * * *
43056 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGAATTTCCAAAATCGCAATGCGAATAAGAAAATCGCAA
** **
43097 TGCGAATTTGGAAAATCGCAATGCGAATTGGAAAATCGCAA
1 TGCGAATTTCCAAAATCGCAATGCGAATAAGAAAATCGCAA
43138 TGCGAATT
1 TGCGAATT
43146 GGAAAAATCG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (41 bp):
TGCGAATTTCCAAAATCGCAATGCGAATAAGAAAATCGCAA
Found at i:43114 original size:21 final size:20
Alignment explanation
Indices: 43071--43158 Score: 131
Period size: 20 Copynumber: 4.3 Consensus size: 20
43061 TTTTCCCAAT
** *
43071 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATTGGAAAA
43091 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TTGGAAAA
43112 TCGCAATGCGAATTGGAAAA
1 TCGCAATGCGAATTGGAAAA
43132 TCGCAATGCGAATTGGAAAAA
1 TCGCAATGCGAATTGG-AAAA
43153 TCGCAA
1 TCGCAA
43159 CGCGGTACTG
Statistics
Matches: 63, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
20 36 0.57
21 27 0.43
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATTGGAAAA
Found at i:43153 original size:41 final size:41
Alignment explanation
Indices: 43071--43158 Score: 133
Period size: 41 Copynumber: 2.1 Consensus size: 41
43061 TTTTCCCAAT
*
43071 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATAAGAAAATCGCAATGCGAATTTGGAAAA
**
43112 TCGCAATGCGAATTGGAAAATCGCAATGCGAA-TTGGAAAAA
1 TCGCAATGCGAATAAGAAAATCGCAATGCGAATTTGG-AAAA
43153 TCGCAA
1 TCGCAA
43159 CGCGGTACTG
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 4 0.09
41 39 0.91
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATAAGAAAATCGCAATGCGAATTTGGAAAA
Found at i:43177 original size:20 final size:20
Alignment explanation
Indices: 43152--43202 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
43142 AATTGGAAAA
43152 ATCGCAACGCGGTACTGACT
1 ATCGCAACGCGGTACTGACT
43172 ATCGCAACGCGGTACTGACT
1 ATCGCAACGCGGTACTGACT
43192 ATCGCAACGCG
1 ATCGCAACGCG
43203 ATAATACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGTACTGACT
Found at i:43217 original size:41 final size:41
Alignment explanation
Indices: 43172--43300 Score: 134
Period size: 41 Copynumber: 3.2 Consensus size: 41
43162 GGTACTGACT
* *
43172 ATCGCAACGCGGTACTGACTATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAAA
* * * * *
43213 ATCGCAACGCGATACTGACTTTCACAACTCGATACT-TAAT
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAAA
* * * * * *
43253 TTCGCAACTCAATACTGAATTTCGCAACGAGATAATACATA
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAAA
43294 ATCGCAA
1 ATCGCAA
43301 TGTGATTTTC
Statistics
Matches: 68, Mismatches: 19, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
40 30 0.44
41 38 0.56
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (41 bp):
ATCGCAACGCGATACTGACTTTCGCAACGCGATAATACAAA
Found at i:43245 original size:20 final size:20
Alignment explanation
Indices: 43214--43280 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
43204 TAATACAAAA
* *
43214 TCGCAACGCGATACTGACTT
1 TCGCAACTCGATACTGAATT
* *
43234 TCACAACTCGATACTTAATT
1 TCGCAACTCGATACTGAATT
*
43254 TCGCAACTCAATACTGAATT
1 TCGCAACTCGATACTGAATT
43274 TCGCAAC
1 TCGCAAC
43281 GAGATAATAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (20 bp):
TCGCAACTCGATACTGAATT
Found at i:43828 original size:20 final size:20
Alignment explanation
Indices: 43779--43837 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
43769 TTTATTCTCT
* **
43779 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
43799 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
43819 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
43838 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:44028 original size:25 final size:24
Alignment explanation
Indices: 43974--44028 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
43964 TGTTTATTAT
* *
43974 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
43998 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
44024 TGTTT
1 TGTTT
44029 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:45173 original size:18 final size:18
Alignment explanation
Indices: 45152--45199 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
45142 TCCACTTCGG
45152 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
45170 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
45188 GAGCCATCACCT
1 GAGCCATCACCT
45200 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:45785 original size:19 final size:20
Alignment explanation
Indices: 45731--45797 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
45721 ATAGTTACTT
* *
45731 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
45751 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
45771 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
45790 TCGCAACG
1 TCGCAACG
45798 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:45824 original size:19 final size:19
Alignment explanation
Indices: 45731--45833 Score: 72
Period size: 19 Copynumber: 5.6 Consensus size: 19
45721 ATAGTTACTT
* **
45731 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
45751 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
45771 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
45790 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
45804 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
45823 TCGCAATGCGA
1 TCGCAACGCGA
45834 TTTGTGTTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.15
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 27 0.40
20 24 0.35
21 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:45924 original size:20 final size:20
Alignment explanation
Indices: 45878--45964 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
45868 GCGATTTTGT
**
45878 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
* *
45897 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTCCG
45917 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
45937 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
45957 CGTTGCGA
1 CGTTGCGA
45965 AAGTAAGTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
19 13 0.22
20 47 0.78
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:45975 original size:20 final size:19
Alignment explanation
Indices: 45891--45990 Score: 83
Period size: 20 Copynumber: 5.1 Consensus size: 19
45881 TGCGATTTTC
* * **
45891 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
* *
45910 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
*
45930 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
45951 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
45970 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
45990 A
1 A
45991 ACTATTCTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
19 5 0.07
20 63 0.89
21 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:45982 original size:40 final size:40
Alignment explanation
Indices: 45891--45984 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
45881 TGCGATTTTC
* * *
45891 ATTT-CGCATTGCGATAGCCATTTCCGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
* *
45930 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
*
45970 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
45985 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.09
40 40 0.85
41 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
Found at i:46362 original size:21 final size:20
Alignment explanation
Indices: 46336--46403 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
46326 CTGTCATTCC
46336 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
46357 TCAAGAGCCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
*
46378 TCAAGAGTCCCC-CCACCGT
1 TCAAGAGTCCCCTCCATCGT
46397 TCAAGAG
1 TCAAGAG
46404 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
19 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.15, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:46415 original size:40 final size:42
Alignment explanation
Indices: 46326--46415 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 42
46316 CCCGACTCAC
* * *
46326 CTGTCATTCCTCAAGAGTCCCCTCCAATCGTTCAAGAGCCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGCCCA
* *
46368 CTATCATCCCTCAAGAGTCCCC-CC-ACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGCCCA
46408 CTGTCATC
1 CTGTCATC
46416 GTTAAGAGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 20 0.48
41 2 0.05
42 20 0.48
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.22
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGCCCA
Found at i:47852 original size:14 final size:14
Alignment explanation
Indices: 47818--47856 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
47808 TTGATTGTTT
47818 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
47832 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
47846 TGTTGATTTGT
1 AATTGATTTGT
47857 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:47994 original size:14 final size:14
Alignment explanation
Indices: 47975--48025 Score: 57
Period size: 14 Copynumber: 3.3 Consensus size: 14
47965 GAAACTGACT
47975 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
47989 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
48008 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
48022 ATCG
1 ATCG
48026 TAATGCGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 15 0.47
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.34
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:48021 original size:19 final size:19
Alignment explanation
Indices: 47985--48021 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
47975 ATCGCAACGA
* *
47985 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
48004 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
48022 ATCGTAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:48077 original size:20 final size:20
Alignment explanation
Indices: 48052--48147 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 20
48042 TCGCATTGCG
*
48052 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
***
48072 ATTTTC-ACGTTGCGATTTTTC
1 ATTTTCGA-GTTGCGA-TAGCC
*
48093 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
48112 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
* *
48132 ATTTTTGCGTTGCGAT
1 ATTTTCGAGTTGCGAT
48148 TTCCCCGTTG
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
19 4 0.06
20 54 0.87
21 4 0.06
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:48147 original size:40 final size:40
Alignment explanation
Indices: 48054--48135 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 40
48044 GCATTGCGAT
* ***
48054 TTTCTAGTTGCGATAGCCATTTTCACGTTGCGATTTTTCA
1 TTTCGAGTTGCGATAGCCATTTTCACGTTGCGATTAGCCA
* *
48094 TTTCGAATTGCGATAGCCATTTTCGCGTTGCGA-TAGCCA
1 TTTCGAGTTGCGATAGCCATTTTCACGTTGCGATTAGCCA
48133 TTT
1 TTT
48136 TTGCGTTGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 6 0.17
40 30 0.83
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (40 bp):
TTTCGAGTTGCGATAGCCATTTTCACGTTGCGATTAGCCA
Found at i:48401 original size:20 final size:20
Alignment explanation
Indices: 48376--48419 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
48366 ATTTTCTCTC
48376 GCGAAAGTCAGAATCTCGTT
1 GCGAAAGTCAGAATCTCGTT
48396 GCGAAAGTCAGAATCTCGTT
1 GCGAAAGTCAGAATCTCGTT
48416 GCGA
1 GCGA
48420 TTTTGTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (20 bp):
GCGAAAGTCAGAATCTCGTT
Found at i:50176 original size:19 final size:19
Alignment explanation
Indices: 50154--50284 Score: 103
Period size: 19 Copynumber: 7.7 Consensus size: 19
50144 GGAAATTACT
50154 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
50173 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
50187 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
50206 ATCGCAACGCG-AAT----
1 ATCGCAATGCGAAATGAAA
*
50220 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
50239 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
50253 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
50272 ATCGCAACGCGAA
1 ATCGCAATGCGAA
50285 TTTAGTTTCG
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
14 28 0.33
15 5 0.06
16 4 0.05
17 4 0.05
18 5 0.06
19 40 0.47
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:50196 original size:33 final size:33
Alignment explanation
Indices: 50154--50280 Score: 211
Period size: 33 Copynumber: 3.8 Consensus size: 33
50144 GGAAATTACT
50154 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
50187 ATCGCAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
50219 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
50253 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
50281 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
32 1 0.01
33 85 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:50261 original size:66 final size:66
Alignment explanation
Indices: 50155--50287 Score: 257
Period size: 66 Copynumber: 2.0 Consensus size: 66
50145 GAAATTACTA
50155 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
50220 T
66 T
*
50221 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
50286 T
66 T
50287 T
1 T
50288 AGTTTCGCGT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:50333 original size:19 final size:19
Alignment explanation
Indices: 50309--50355 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
50299 GCGATTTTGT
*
50309 CGTTGCTATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
50328 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTCATTTCG
*
50347 CATTGCGAT
1 CGTTGCGAT
50356 AGTACTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.19, G:0.19, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:50481 original size:14 final size:14
Alignment explanation
Indices: 50462--50498 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
50452 CATCAATTAA
50462 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
50476 ACAAATCACCTTTT
1 ACAAATCAACTTTT
50490 ACAAATCAA
1 ACAAATCAA
50499 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:51908 original size:21 final size:21
Alignment explanation
Indices: 51842--51908 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
51832 GTGAATCGGG
*
51842 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
51862 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
51884 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
51905 CTCT
1 CTCT
51909 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:52355 original size:91 final size:89
Alignment explanation
Indices: 52180--52359 Score: 272
Period size: 91 Copynumber: 2.0 Consensus size: 89
52170 ATTTCAAACT
*
52180 TTCAACCAAAAGCAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATATACAGTTTAGCA
1 TTCAACCAAAAGCAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGCA
52245 GAATTGGCAACAACCGAATAAATTCAC
63 GAATTGGCAACAACCGAATAAATTCAC
52272 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAG-CAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
52336 GTATTGGCAGCAACCGAATAAATT
63 GAATTGGCAACAACCGAATAAATT
52360 TACTAAGCAA
Statistics
Matches: 82, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
91 37 0.45
92 12 0.15
93 6 0.07
95 27 0.33
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (89 bp):
TTCAACCAAAAGCAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGAA
TTGGCAACAACCGAATAAATTCAC
Found at i:54102 original size:34 final size:33
Alignment explanation
Indices: 54035--54124 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 33
54025 TCTTTTGGTT
54035 GAAATGAAAATCGCAACAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAAC-G---A-GAGAATCGCAACGC
**
54073 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
54107 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
54125 CGAAATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 16 0.34
34 14 0.30
35 1 0.02
38 1 0.02
39 15 0.32
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:54120 original size:19 final size:19
Alignment explanation
Indices: 54035--54146 Score: 110
Period size: 19 Copynumber: 6.1 Consensus size: 19
54025 TCTTTTGGTT
*
54035 GAAATGAAAATCGCAAC-A
1 GAAATGAAAATCGCAACGC
*
54053 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
54073 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
54091 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
54107 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
54126 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
54145 GA
1 GA
54147 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.12
15 1 0.01
16 2 0.03
17 1 0.01
18 4 0.05
19 47 0.60
20 12 0.15
21 2 0.03
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:54848 original size:21 final size:20
Alignment explanation
Indices: 54817--54867 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
54807 ATAGTCAGTA
*
54817 TCGCA-TGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
**
54837 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
54857 TCGCATTGCGA
1 TCGCATTGCGA
54868 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:54909 original size:21 final size:22
Alignment explanation
Indices: 54857--54909 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
54847 ATTTACTTAT
54857 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
54878 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
54899 TCGCATTGCGA
1 TCGCATTGCGA
54910 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:56560 original size:25 final size:25
Alignment explanation
Indices: 56517--56583 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
56507 AGTTGTTTAG
* * * * *
56517 TAAAATATTAATAAATTTTAGTAGT
1 TAAAATATTATTTATTTTTAATAAT
56542 TAAAATTATT-TTTATTTTTAATAAT
1 TAAAA-TATTATTTATTTTTAATAAT
*
56567 TAATATATTATTTATTT
1 TAAAATATTATTTATTT
56584 GTAAAGGTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
24 4 0.12
25 26 0.76
26 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
TAAAATATTATTTATTTTTAATAAT
Found at i:57066 original size:19 final size:19
Alignment explanation
Indices: 57031--57152 Score: 72
Period size: 21 Copynumber: 6.1 Consensus size: 19
57021 TAAACAAAAC
57031 ACAAAAAAAGGAT-AAAATAA
1 ACAAAAAAA--ATAAAAATAA
**
57051 GTAAAAAAAATAAAAATAA
1 ACAAAAAAAATAAAAATAA
57070 ACAAAAAAAATGATAACAA-AA
1 ACAAAAAAAAT-A-AA-AATAA
57091 A-AACAAAAAATAATAAATAA
1 ACAA-AAAAAATAA-AAATAA
* * *
57111 ATAAAATAAAACAAATATGAA
1 ACAAAA-AAAATAAAAAT-AA
57132 ACGAAAATAAAAT-AAAATAA
1 AC-AAAA-AAAATAAAAATAA
57152 A
1 A
57153 TGGAATTAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.02
19 19 0.23
20 23 0.28
21 27 0.33
22 11 0.13
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (19 bp):
ACAAAAAAAATAAAAATAA
Found at i:57126 original size:18 final size:18
Alignment explanation
Indices: 57042--57224 Score: 83
Period size: 18 Copynumber: 9.9 Consensus size: 18
57032 CAAAAAAAGG
*
57042 ATAAAATAAGTAAAAAAA
1 ATAAAATAAATAAAAAAA
*
57060 ATAAAAATAAACAAAAAAA
1 AT-AAAATAAATAAAAAAA
* *
57079 ATGATAACAAA-AAAACAAA
1 AT-AAAATAAATAAAA-AAA
*
57098 A-AATAATAAATAAATAAA
1 ATAA-AATAAATAAAAAAA
*
57116 ATAAAACAAATATGAAACGAAA
1 ATAAAATAAATA--AAA--AAA
***
57138 ATAAAATAAAATAAATGGA
1 ATAAAAT-AAATAAAAAAA
* *
57157 ATTAAATAAA-AAACACAA
1 ATAAAATAAATAAA-AAAA
*
57175 ATAAGA-AAATAAGAAAAA
1 ATAAAATAAATAA-AAAAA
*
57193 ATAAAA-AAA-AAATAAA
1 ATAAAATAAATAAAAAAA
*
57209 A-AGAATAAAGTAAAAA
1 ATAAAATAAA-TAAAAA
57225 TAAGTACAAA
Statistics
Matches: 124, Mismatches: 25, Indels: 32
0.69 0.14 0.18
Matches are distributed among these distances:
15 3 0.02
16 8 0.06
17 9 0.07
18 47 0.38
19 39 0.31
20 2 0.02
21 2 0.02
22 9 0.07
23 5 0.04
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (18 bp):
ATAAAATAAATAAAAAAA
Found at i:57197 original size:31 final size:31
Alignment explanation
Indices: 57160--57227 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
57150 AAATGGAATT
*
57160 AAATAAAAAACACAAATAAGAA-AAT-AAGAAA
1 AAATAAAAAA-A-AAATAAAAAGAATAAAGAAA
*
57191 AAATAAAAAAAAAATAAAAAGAATAAAGTAA
1 AAATAAAAAAAAAATAAAAAGAATAAAGAAA
57222 AAATAA
1 AAATAA
57228 GTACAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 8 0.24
30 4 0.12
31 21 0.64
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (31 bp):
AAATAAAAAAAAAATAAAAAGAATAAAGAAA
Found at i:57224 original size:21 final size:21
Alignment explanation
Indices: 57180--57238 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
57170 CACAAATAAG
57180 AAAATAAGAAAAAATAAAAAA
1 AAAATAAGAAAAAATAAAAAA
* **
57201 AAAATAA-AAAGAATAAAGTA
1 AAAATAAGAAAAAATAAAAAA
57221 AAAATAAGTACAAAAATA
1 AAAATAAG-A-AAAAATA
57239 TACAATACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 17 0.55
21 7 0.23
22 1 0.03
23 6 0.19
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.14
Consensus pattern (21 bp):
AAAATAAGAAAAAATAAAAAA
Found at i:57329 original size:14 final size:14
Alignment explanation
Indices: 57307--57348 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
57297 ATATATATAT
*
57307 ATAAGTAAATAAAA
1 ATAAATAAATAAAA
*
57321 ATAAATAAATAAAT
1 ATAAATAAATAAAA
*
57335 ATTAAT-AATAAAA
1 ATAAATAAATAAAA
57348 A
1 A
57349 ATTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (14 bp):
ATAAATAAATAAAA
Found at i:59483 original size:83 final size:84
Alignment explanation
Indices: 59231--59488 Score: 339
Period size: 83 Copynumber: 3.1 Consensus size: 84
59221 ATATAATTCA
* *
59231 AAGGTCTTT-GTTGGCAGATAGACT-TTCTTGCCTTGAGCTATGCTGCAAATGATGCG--TTTGA
1 AAGGTCTTTGGTTGGCAGATAG-CTCTTCTTGACTTAAGCTATGCTGCAAATGATGCGCCTTTGA
*
59292 GCTGAGTGTAATCGAACTCG
65 GCTGAGTGTAATCAAACTCG
* * * ** * * *
59312 AAGGTATTTTGTTGGCAGATAAC-CTTCTCAACTTAAGTTATGCTGCAAATGGTGCACCTTTGAG
1 AAGGTCTTTGGTTGGCAGATAGCTCTTCTTGACTTAAGCTATGCTGCAAATGATGCGCCTTTGAG
59376 CTGAGTGTAATCAAACTCG
66 CTGAGTGTAATCAAACTCG
*
59395 AAGGTCTTTGGTTGGCAGATAGCTCTTCTTGACTTAAGCTATACTGCAAATGATGCGCCTTTGAG
1 AAGGTCTTTGGTTGGCAGATAGCTCTTCTTGACTTAAGCTATGCTGCAAATGATGCGCCTTTGAG
* *
59460 -TGAGTGTAATTAAACTCT
66 CTGAGTGTAATCAAACTCG
59478 AAGGTCTTTGG
1 AAGGTCTTTGG
59489 CAGATAACCT
Statistics
Matches: 151, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
81 34 0.23
82 11 0.07
83 71 0.47
84 35 0.23
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (84 bp):
AAGGTCTTTGGTTGGCAGATAGCTCTTCTTGACTTAAGCTATGCTGCAAATGATGCGCCTTTGAG
CTGAGTGTAATCAAACTCG
Found at i:59589 original size:31 final size:32
Alignment explanation
Indices: 59552--59644 Score: 107
Period size: 31 Copynumber: 2.8 Consensus size: 32
59542 GTAGTCAAAC
*
59552 TCAAAGGTCTTTGTGTTTCAAGAGAAAC-ATT
1 TCAAAGGTTTTTGTGTTTCAAGAGAAACGATT
* * *
59583 TTAAAGGTTTTTTTTTTTCAAGAGAAACGATT
1 TCAAAGGTTTTTGTGTTTCAAGAGAAACGATT
*
59615 TCAAAGATTTTTTTTGTGTTTCAAGAGAAA
1 TCAAAG---GTTTTTGTGTTTCAAGAGAAA
59645 TTGTCCCCAG
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
31 24 0.48
32 8 0.16
35 18 0.36
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (32 bp):
TCAAAGGTTTTTGTGTTTCAAGAGAAACGATT
Found at i:59781 original size:36 final size:36
Alignment explanation
Indices: 59698--60143 Score: 357
Period size: 36 Copynumber: 12.8 Consensus size: 36
59688 CAAAGGTTGG
* * *
59698 TGTTTCAAGAGAAATTGTATCAAGAGAGACAAAACTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
59735 TGTTTCAAGGGAAACTGTCTCAATAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
59771 TGTTTAAAGGGAAACTGTCTCAAGAGAGATAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* **
59807 TG-TTCAAGAGAAACTGTCTCAAGAGAGATGAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
59842 TGTTTCAAGGAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAATT
*
59871 TGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
59907 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * *
59942 TGTATCAAGAGAAAACTGTCTCAAGAGAGACAAAGACAAAAT
1 TGTTTCAAG-GGAAACTGTCTCAAGAGAGAC----A-AAATT
* *
59984 TGTTTCAAGAGAAACTGTCTCAAGAAAGAC-AAATCT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-T
* ** *
60020 TAGTTCCAAAAGAAACTG--TCAAGGGAGACAAAATT
1 T-GTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * *
60055 TGTTT-AATGTAAAACATAT-TC-------A-AAATTT
1 TGTTTCAA-GGGAAAC-TGTCTCAAGAGAGACAAAATT
60083 TGTTTCAAGGGAAA-TGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
60118 T-TTTCAAAGGAAACTGTTTCAAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGA
60144 AACTGTCTCA
Statistics
Matches: 334, Mismatches: 41, Indels: 70
0.75 0.09 0.16
Matches are distributed among these distances:
26 2 0.01
27 2 0.01
28 16 0.05
29 23 0.07
30 1 0.00
31 1 0.00
32 2 0.01
33 4 0.01
34 20 0.06
35 78 0.23
36 109 0.33
37 46 0.14
41 18 0.05
42 12 0.04
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:59887 original size:100 final size:101
Alignment explanation
Indices: 59769--59957 Score: 301
Period size: 100 Copynumber: 1.9 Consensus size: 101
59759 AGAGACAAAA
* *
59769 TTTGTTTAAAGGGAAACTGTCTCAAGAGAGATAAAATTTG-TTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTAAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* *
59833 GATGAAATTTGTTTCAAG-GAAAACATATTCAAAGAT
66 GA-CAAATTTGTATCAAGAGAAAACATATTCAAAGAT
* *
59869 TTTGTTTCAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTAAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
59934 GACAAATTTGTATCAAGAGAAAAC
66 GACAAATTTGTATCAAGAGAAAAC
59958 TGTCTCAAGA
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 50 0.62
101 31 0.38
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (101 bp):
TTTGTTTAAAGGAAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GACAAATTTGTATCAAGAGAAAACATATTCAAAGAT
Found at i:59929 original size:172 final size:177
Alignment explanation
Indices: 59666--60008 Score: 486
Period size: 172 Copynumber: 1.9 Consensus size: 177
59656 GAGGCAACAT
* *
59666 TTTGTTTCAAGAGAAACATATTCAAAGGTTGGTGTTTCAAGAGAAATTGTATCAAGAGAGACAAA
1 TTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTGTATCAAGAGAGACAAA
* * *
59731 ACTTTGTTTCAAGGGAAACTGTCTCAATAGAGACAAAATTTGTTTAAAG-GGAAACTGTCTCAAG
66 ACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAATTTGTATAAAGAGAAAACTGTCTCAAG
* *
59795 AGAG-ATA-AAATTTG-TTCAAGAGAAACTGTCTCAAGAGAGATGAAA
130 AGAGAAGACAAAATTGTTTCAAGAGAAACTGTCTCAAGAGAGATGAAA
* *
59840 TTTGTTTCAAG-GAAAACATATTCAAAGATT-TTGTTTCAAG-GAAAACTGTCTCAAGAGAGACA
1 TTTGTTTCAAGAG-AAACATATTCAAAGATTGGTGTTTCAAGAG-AAACTGTATCAAGAGAGACA
*
59902 AAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTGTATCAAGAGAAAACTGTCTCAA
64 AAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTGTATAAAGAGAAAACTGTCTCAA
59966 GAGAGACAAAGACAAAATTGTTTCAAGAGAAACTGTCTCAAGA
129 GAGAG---AAGACAAAATTGTTTCAAGAGAAACTGTCTCAAGA
60009 AAGACAAATC
Statistics
Matches: 150, Mismatches: 10, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
171 12 0.08
172 50 0.33
173 31 0.21
174 27 0.18
176 2 0.01
177 6 0.04
178 22 0.15
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (177 bp):
TTTGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAACTGTATCAAGAGAGACAAA
ACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAATTTGTATAAAGAGAAAACTGTCTCAAGA
GAGAAGACAAAATTGTTTCAAGAGAAACTGTCTCAAGAGAGATGAAA
Found at i:59967 original size:16 final size:17
Alignment explanation
Indices: 59918--59969 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
59908 GTTTCAAGGG
59918 AAACTGTCTCAAGAGAGAC
1 AAACTGTCTC-A-AGAGAC
* *
59937 AAATTTGTATCAAGAGA-
1 AAA-CTGTCTCAAGAGAC
59954 AAACTGTCTCAAGAGA
1 AAACTGTCTCAAGAGA
59970 GACAAAGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 5 0.18
19 4 0.14
20 5 0.18
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (17 bp):
AAACTGTCTCAAGAGAC
Found at i:60057 original size:213 final size:206
Alignment explanation
Indices: 59698--60143 Score: 562
Period size: 213 Copynumber: 2.1 Consensus size: 206
59688 CAAAGGTTGG
* * * * *
59698 TGTTTCAAGAGAAATTGTATCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAATAGAG
1 TGTTTCAAGGGAAACTGTATCAAGAGAGACAAAACTTTGTATCAAGGAAAACTGTCTCAAGAGAG
* * * *
59763 ACAAAATTTGTTTAAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTCAAGAGAAACTGTCTCA
66 ACAAAAATTGTTTAAAGAGAAACTGTCTCAAGAAAGATAAAATTTGTTCAAAAGAAACTG-CTCA
**
59828 AGAGAGATGAAATTTGTTTCAA-GGAAAACATATTCAAAGATTTTGTTTCAAGGAAAACTGTCTC
130 AGAGAGACAAAATTTGTTT-AATGGAAAACATATTCAAA-ATTTTGTTTCAAGGAAAA-TGTCTC
59892 AAGAGAGACAAAATT
192 AAGAGAGACAAAATT
*
59907 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAA-TTTGTATCAAGAGAAAACTGTCTCAAGAGA
1 TGTTTCAAGGGAAACTGTATCAAGAGAGACAAAACTTTGTATCAAG-GAAAACTGTCTCAAGAGA
* *
59970 GACAAAGACAAAATTGTTTCAAGAGAAACTGTCTCAAGAAAGA-CAAATCTTAGTTCCAAAAGAA
65 GAC----A-AAAATTGTTTAAAGAGAAACTGTCTCAAGAAAGATAAAAT-TT-GTT-CAAAAGAA
* * *
60034 ACTG-TCAAGGGAGACAAAATTTGTTTAATGTAAAACATATTCAAAATTTTGTTTCAAGGGAAAT
122 ACTGCTCAAGAGAGACAAAATTTGTTTAATGGAAAACATATTCAAAATTTTGTTTCAAGGAAAAT
60098 GTCTCAAGAGAGACAAAATT
187 GTCTCAAGAGAGACAAAATT
* *
60118 T-TTTCAAAGGAAACTGTTTCAAGAGA
1 TGTTTCAAGGGAAACTGTATCAAGAGA
60144 AACTGTCTCA
Statistics
Matches: 208, Mismatches: 19, Indels: 19
0.85 0.08 0.08
Matches are distributed among these distances:
207 10 0.05
208 22 0.11
209 27 0.13
210 23 0.11
211 22 0.11
212 24 0.12
213 66 0.32
214 3 0.01
215 11 0.05
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (206 bp):
TGTTTCAAGGGAAACTGTATCAAGAGAGACAAAACTTTGTATCAAGGAAAACTGTCTCAAGAGAG
ACAAAAATTGTTTAAAGAGAAACTGTCTCAAGAAAGATAAAATTTGTTCAAAAGAAACTGCTCAA
GAGAGACAAAATTTGTTTAATGGAAAACATATTCAAAATTTTGTTTCAAGGAAAATGTCTCAAGA
GAGACAAAATT
Found at i:60123 original size:34 final size:37
Alignment explanation
Indices: 60075--60143 Score: 99
Period size: 35 Copynumber: 1.9 Consensus size: 37
60065 AAAACATATT
*
60075 CAAAATTTTGTTTCAAGGGAAA-TGTCTCAAGAGAGA
1 CAAAATTTTGTTTCAAAGGAAACTGTCTCAAGAGAGA
*
60111 CAAAA-TTT-TTTCAAAGGAAACTGTTTCAAGAGA
1 CAAAATTTTGTTTCAAAGGAAACTGTCTCAAGAGA
60144 AACTGTCTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 11 0.37
35 14 0.47
36 5 0.17
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.29
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAAGGAAACTGTCTCAAGAGAGA
Found at i:60139 original size:15 final size:16
Alignment explanation
Indices: 60119--60160 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
60109 GACAAAATTT
60119 TTTCAAAG-GAAACTG
1 TTTCAAAGAGAAACTG
60134 TTTC-AAGAGAAACTG
1 TTTCAAAGAGAAACTG
*
60149 TCTCAAGAGAGA
1 TTTCAA-AGAGA
60161 CAAAACTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 14 0.61
16 1 0.04
17 5 0.22
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.24
Consensus pattern (16 bp):
TTTCAAAGAGAAACTG
Done.