Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006723.1 Hibiscus syriacus cultivar Beakdansim tig00016841_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: 149344
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5000 original size:3 final size:3
Alignment explanation
Indices: 4994--5018 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4984 CTTCTTCTTC
4994 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
5019 TATCATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:13488 original size:39 final size:39
Alignment explanation
Indices: 13433--13667 Score: 105
Period size: 34 Copynumber: 6.5 Consensus size: 39
13423 ATATACACAT
* * * *
13433 ATATATATTATCTAGTTTGCAAATTGTTTTTGAAAATAC
1 ATATATAATATATAGTTTGCAAAATATTTTTGAAAATAC
**
13472 ATATATAATATATAGTTTTTAAAATATTTTTG--AA-A-
1 ATATATAATATATAGTTTGCAAAATATTTTTGAAAATAC
* ** *
13507 ATATGT-ATATATAGTTTTTAAAACATTTTTG-AAAT--
1 ATATATAATATATAGTTTGCAAAATATTTTTGAAAATAC
**
13542 -TATATAATATATAGTTTTG-AAAACGTTTTT---AA-A-
1 ATATATAATATATAG-TTTGCAAAATATTTTTGAAAATAC
** * * *
13575 ATATATAATATATAGTTTTG-AAAA-CGTTATGAAAACAT
1 ATATATAATATATAG-TTTGCAAAATATTTTTGAAAATAC
* * * **
13613 TTATATATTATATAATTTTTAAAATCA-TTTTGAAAAT--
1 ATATATAATATATAGTTTGCAAAAT-ATTTTTGAAAATAC
13650 ATATATAATATATAGTTT
1 ATATATAATATATAGTTT
13668 TTTTAAAACA
Statistics
Matches: 158, Mismatches: 24, Indels: 30
0.75 0.11 0.14
Matches are distributed among these distances:
33 5 0.03
34 51 0.32
35 25 0.16
36 6 0.04
37 21 0.13
38 16 0.10
39 34 0.22
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (39 bp):
ATATATAATATATAGTTTGCAAAATATTTTTGAAAATAC
Found at i:13517 original size:41 final size:39
Alignment explanation
Indices: 13431--13667 Score: 111
Period size: 39 Copynumber: 6.5 Consensus size: 39
13421 ATATATACAC
* * * *
13431 ATATATATATTATCTAGTTTGCAAATTGTTTTTGAAAAT
1 ATATATATAATATATAGTTTGCAAAATATTTTTGAAAAT
* **
13470 ACATATATAATATATAGTTTTTAAAATATTTTTGAAAAT
1 ATATATATAATATATAGTTTGCAAAATATTTTTGAAAAT
* *
13509 ATGTATAT-ATAGT-T--TTT--AAAACATTTTTG--AA-
1 ATATATATAATA-TATAGTTTGCAAAATATTTTTGAAAAT
**
13540 AT-TATATAATATATAGTTTTG-AAAACGTTTTT---AA-
1 ATATATATAATATATAG-TTTGCAAAATATTTTTGAAAAT
** * *
13574 A-ATATATAATATATAGTTTTG-AAAA-CGTTATGAAAAC
1 ATATATATAATATATAG-TTTGCAAAATATTTTTGAAAAT
* * * **
13611 ATTTATATATTATATAATTTTTAAAATCA-TTTTG-AAA-
1 ATATATATAATATATAGTTTGCAAAAT-ATTTTTGAAAAT
13648 ATATATATAATATATAGTTT
1 ATATATATAATATATAGTTT
13668 TTTTAAAACA
Statistics
Matches: 159, Mismatches: 23, Indels: 34
0.74 0.11 0.16
Matches are distributed among these distances:
30 6 0.04
31 6 0.04
32 2 0.01
33 3 0.02
34 40 0.25
35 10 0.06
36 5 0.03
37 21 0.13
38 23 0.14
39 43 0.27
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (39 bp):
ATATATATAATATATAGTTTGCAAAATATTTTTGAAAAT
Found at i:13559 original size:35 final size:35
Alignment explanation
Indices: 13473--13712 Score: 220
Period size: 34 Copynumber: 6.7 Consensus size: 35
13463 TGAAAATACA
* *
13473 TATATAATATATAGTTTTTAAAATATTTTTGAAAA
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAT
*
13508 TATGT-ATATATAGTTTTTAAAACATTTTTGAAAT
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAT
* * *
13542 TATATAATATATAGTTTTGAAAACGTTTTT-AAAA
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAT
* * *
13576 TATATAATATATAGTTTTGAAAAC-GTTATGAAAACATT
1 TATATAATATATAGTTTTTAAAACATTTTTG--AA-A-T
* *
13614 TATATATTATATAATTTTTAAAATCA-TTTTGAAAAT
1 TATATAATATATAGTTTTTAAAA-CATTTTTG-AAAT
**
13650 ATATATAATATATAGTTTTTTTAAAACATTTTAAAAACT
1 -TATATAATATATAG--TTTTTAAAACATTTTTGAAA-T
*
13689 TATATATTATAT-GTTTTTGAAAAC
1 TATATAATATATAGTTTTT-AAAAC
13713 GTTTATATAT
Statistics
Matches: 172, Mismatches: 19, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
33 3 0.02
34 58 0.34
35 31 0.18
36 8 0.05
37 15 0.09
38 39 0.23
39 18 0.10
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (35 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAT
Found at i:13619 original size:38 final size:36
Alignment explanation
Indices: 13513--13716 Score: 157
Period size: 38 Copynumber: 5.6 Consensus size: 36
13503 GAAAATATGT
* * ***
13513 ATATATAGTTTTTAAAACATTTTTGAAA-TTATATA
1 ATATATAGTTTTGAAAACGTTTGAAAAATTTATATA
**
13548 ATATATAGTTTTGAAAACGTTTTTAAAA--TATATA
1 ATATATAGTTTTGAAAACGTTTGAAAAATTTATATA
13582 ATATATAGTTTTGAAAACGTTATGAAAACATTTATATA
1 ATATATAGTTTTGAAAACGTT-TGAAAA-ATTTATATA
* * * * *
13620 TTATATAATTTTTAAAATCATTTTG-AAAATATATATA
1 ATATATAGTTTTGAAAA-C-GTTTGAAAAATTTATATA
* * * *
13657 ATATATAGTTTTTTTAAAACATTTTAAAAACTTATATA
1 ATATATAG--TTTTGAAAACGTTTGAAAAATTTATATA
*
13695 TTATAT-GTTTTTGAAAACGTTT
1 ATATATAG-TTTTGAAAACGTTT
13717 ATATATATAA
Statistics
Matches: 141, Mismatches: 19, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
34 27 0.19
35 29 0.21
36 14 0.10
37 18 0.13
38 39 0.28
39 12 0.09
40 2 0.01
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (36 bp):
ATATATAGTTTTGAAAACGTTTGAAAAATTTATATA
Found at i:14958 original size:6 final size:6
Alignment explanation
Indices: 14947--14976 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
14937 CAATTCCATT
14947 TTTTTA TTTTTA TTTTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA -TTTTTA TTTTTA TTTTT
14977 TTTGGTCCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:14964 original size:13 final size:13
Alignment explanation
Indices: 14946--14977 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
14936 TCAATTCCAT
14946 TTTTTTATTTTTA
1 TTTTTTATTTTTA
14959 TTTTTTATTTTTA
1 TTTTTTATTTTTA
14972 TTTTTT
1 TTTTTT
14978 TTGGTCCCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:19634 original size:94 final size:94
Alignment explanation
Indices: 19501--20810 Score: 2341
Period size: 94 Copynumber: 13.9 Consensus size: 94
19491 ATATCGTGCC
* * * ** *
19501 ACTCGAGACAACACAAGTTCAACTTCACGACGATGGGACCGCTAATTGTCAATAAACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
19566 AATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
* *
19595 ACTCCAGACAATGCAAGTTCAACTTCACGACGGAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
19660 AATTTCAACTTTGCAATGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
19689 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
19754 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
19783 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
19848 AATTTTAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
19877 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
19942 AATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
19971 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
20036 AATTTCAACTTCGTAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
20065 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
20130 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
20159 ACTCCAGACAACGCAAGTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
20224 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
20253 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
20318 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
20347 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
20412 AATTTCAACTTCGCAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
20441 ACTCCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
20506 AATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
20535 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
20600 AATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
*
20629 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
20694 AATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAACTTCGCAACGAAGGATATTGG
20723 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC-
** * *
20788 CGGTTTCAACTTCACTACGAAGG
65 CAATTTCAACTTCGCAACGAAGG
20811 GAATCGTGCC
Statistics
Matches: 1173, Mismatches: 42, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
94 1153 0.98
95 20 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (94 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAACTTCGCAACGAAGGATATTGG
Found at i:20956 original size:80 final size:80
Alignment explanation
Indices: 20823--21100 Score: 403
Period size: 80 Copynumber: 3.4 Consensus size: 80
20813 ATCGTGCCGA
20823 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
20888 GAGAAGGGCTATCTG
66 GAGAAGGGCTATCTG
* * *
20903 CCAAAGACCTTTGAGTTCGACTCCGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
20968 GAGAAGGGCTATCTG
66 GAGAAGGGCTATCTG
* * * * *
20983 CCAAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGT
*
21048 CGAGAAGGGTTATCTG
65 CGAGAAGGGCTATCTG
* * *
21064 TCAACCGAAGACCTTCGAGTTCGATTACACTCAGCTC
1 ----CCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
21101 AGAGGCAAAC
Statistics
Matches: 180, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
80 104 0.58
81 44 0.24
84 2 0.01
85 30 0.17
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (80 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTC
GAGAAGGGCTATCTG
Found at i:21160 original size:161 final size:156
Alignment explanation
Indices: 20831--21184 Score: 352
Period size: 161 Copynumber: 2.2 Consensus size: 156
20821 GACCAAAGAC
* * * *
20831 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG
1 CTTCGAGTTCGATTACACTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * * *
20896 CTATCTGCCAAAGACCTTTGAGTTCGACTCCGCTCAGCTCCAAGGCATATCATTTGCAGCATAGC
66 CTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCAAACCA--T--AGCATAGC
* * * * * * *
20961 TTAAGTCGAGAAGGGCTATCTGCCAAAGAC
127 TCAAGGCAAGAAGAGCTATATGCCAAAAAA
*
20991 CTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
1 CTTCGAGTTCGATTACACTCAGC-TCGAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGG
* * * **
21056 GTTATCTGTCAACCGAAGACCTTCGAGTTCGATTACACTCAGCT-CAGAGGCAAACCA-AGTTTA
65 GCTATCTG----CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCA-AGGCAAACCATAGCATA
*
21119 GCTCAAGGCAAGAAGAGCTATATGTCAAAAAA
125 GCTCAAGGCAAGAAGAGCTATATGCCAAAAAA
* * * *
21151 TTGTCGAGTTCGATTCCAATCAGCTCGATGGCAC
1 CT-TCGAGTTCGATTACACTCAGCTCGAAGGCAC
21185 CTCAATCACA
Statistics
Matches: 160, Mismatches: 27, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
160 59 0.37
161 64 0.40
164 2 0.01
165 35 0.22
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (156 bp):
CTTCGAGTTCGATTACACTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGG
CTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCAAACCATAGCATAGCTCAA
GGCAAGAAGAGCTATATGCCAAAAAA
Found at i:21761 original size:38 final size:37
Alignment explanation
Indices: 21689--21950 Score: 277
Period size: 38 Copynumber: 7.0 Consensus size: 37
21679 TTGCAAATTG
21689 TTTTTGAAAATACATATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAAT--ATATATAATATATAGTTTTTAAAACA
* *
21728 TTTTTTGAAAATATGTATATTATATAGTTTTTAAAACA
1 -TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
*
21766 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTTGAAAATATATATAATATATAGTTTTT-AAAACA
*
21803 TTTTT-AAAATATATATAATATATAGTTTTGAAAAC-
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* * * * *
21838 GTTATGAAAACATTTATATATTATATAATTTTTAAAATCA
1 TTTTTG-AAA-ATATATATAATATATAGTTTTTAAAA-CA
21878 -TTTTGAAAATATATATAATATATAGTTTTTTTAAAACA
1 TTTTTGAAAATATATATAATATATAG--TTTTTAAAACA
* *
21916 -TTTTAAAAACT-TATATATTATAT-GTTTTTGAAAAC
1 TTTTTGAAAA-TATATATAATATATAGTTTTT-AAAAC
21951 GTTTATATAT
Statistics
Matches: 193, Mismatches: 18, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
35 8 0.04
36 32 0.17
37 57 0.30
38 70 0.36
39 15 0.08
40 11 0.06
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:21870 original size:75 final size:71
Alignment explanation
Indices: 21703--21954 Score: 274
Period size: 75 Copynumber: 3.4 Consensus size: 71
21693 TGAAAATACA
* * *
21703 TATATAATATATAGTTTTTAAAACATTTTTTGAAAATATGTATATTATATAGTTTTTAAAACATT
1 TATATAATATATAGTTTTTAAAAC-GTTTTT-AAAATATATATAATATATAGTTTTTAAAACA--
21768 TTTG-AAAAT
62 TTTGAAAAAT
* *
21777 TATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATAGTTTTGAAAACGTTA
1 TATATAATATATAGTTTTT-AAAACGTTTTTAAAATATATATAATATATAGTTTTTAAAACATT-
21842 TGAAAACATT
64 TGAAAA-A-T
* * * *
21852 TATATATTATATAATTTTTAAAATCATTTTGAAAATATATATAATATATAGTTTTTTTAAAACAT
1 TATATAATATATAGTTTTTAAAA-CGTTTTTAAAATATATATAATATATAG--TTTTTAAAACAT
*
21917 TTTAAAAACT
63 TTGAAAAA-T
*
21927 TATATATTATAT-GTTTTTGAAAACGTTT
1 TATATAATATATAGTTTTT-AAAACGTTT
21955 ATATATATAA
Statistics
Matches: 154, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
71 2 0.01
72 2 0.01
73 30 0.19
74 38 0.25
75 66 0.43
76 5 0.03
77 11 0.07
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (71 bp):
TATATAATATATAGTTTTTAAAACGTTTTTAAAATATATATAATATATAGTTTTTAAAACATTTG
AAAAAT
Found at i:22574 original size:5 final size:5
Alignment explanation
Indices: 22564--22588 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
22554 AAAAACCGAG
22564 GCAAA GCAAA GCAAA GCAAA GCAAA
1 GCAAA GCAAA GCAAA GCAAA GCAAA
22589 TCGAAGAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (5 bp):
GCAAA
Found at i:23205 original size:13 final size:13
Alignment explanation
Indices: 23187--23218 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
23177 CAATTCCATT
23187 TTTTTTAATTTTA
1 TTTTTTAATTTTA
*
23200 TTTTTTATTTTTA
1 TTTTTTAATTTTA
23213 TTTTTT
1 TTTTTT
23219 TTGGTCCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTAATTTTA
Found at i:23539 original size:12 final size:13
Alignment explanation
Indices: 23522--23552 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
23512 TCGAATCGAG
23522 TAATTTAAA-TTT
1 TAATTTAAATTTT
23534 TAATTTAAATTTT
1 TAATTTAAATTTT
23547 TAATTT
1 TAATTT
23553 TTCGCAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
TAATTTAAATTTT
Found at i:28566 original size:23 final size:22
Alignment explanation
Indices: 28507--28569 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
28497 CCAAACGACC
* *
28507 GAAAACGTGCCATAGATATAGA
1 GAAAACGTGCCATAAAGATAGA
** *
28529 GAAAAATATGTCATAAAGATAGAA
1 G-AAAACGTGCCATAAAGATAG-A
28553 GAAAACGTGCCATAAAG
1 GAAAACGTGCCATAAAG
28570 GAAAAAATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
22 1 0.03
23 28 0.90
24 2 0.06
ACGTcount: A:0.51, C:0.11, G:0.21, T:0.17
Consensus pattern (22 bp):
GAAAACGTGCCATAAAGATAGA
Found at i:33766 original size:224 final size:225
Alignment explanation
Indices: 33303--33788 Score: 913
Period size: 225 Copynumber: 2.2 Consensus size: 225
33293 TCTACCATAC
* *
33303 TGCATCCCGATGATGATG-ATATGCATTGTTAAAAGTAGTGACTGATTGATTAATGATAGGTTGA
1 TGCATCCTGATGATGATGAATATGCATTGTTAAAAGTAGTGACTGATTGATTAATGATAGGTCGA
33367 CGATAAATACATGATATTGAGGGATGCAAAAGGAAATTTTTTTATATTGTTCATCTTTGAAAACA
66 CGATAAATACATGATATTGAGGGATGCAAAAGGAAATTTTTTTATATTGTTCATCTTTGAAAACA
*
33432 TCTTTAGTTAACATTAATGAGATTTGCATCTTGTATGCAATTCTATGTGTTTAATATTGTTAGCA
131 TCTTTAGTTAACATTAATCAGATTTGCATCTTGTATGCAATTCTATGTGTTTAATATTGTTAGCA
33497 ATGAGGCCTGCTGGTTTTATCATACTATTT
196 ATGAGGCCTGCTGGTTTTATCATACTATTT
33527 TGCATCCTGATGATGATGAATATGCATTGTTAAAAGTAGTGACTGATTGATTAATGATAGGTCGA
1 TGCATCCTGATGATGATGAATATGCATTGTTAAAAGTAGTGACTGATTGATTAATGATAGGTCGA
33592 CGATAAATACATGATATTGAGGGATGCAAAAGGAAATTTTTTTATATTGTTCATCTTTGAAAACA
66 CGATAAATACATGATATTGAGGGATGCAAAAGGAAATTTTTTTATATTGTTCATCTTTGAAAACA
33657 TCTTTAGTTAACATTAATCAGATTTGCATCTTGTATGCAATTCTATGT-TTTAATATTGTTAGCA
131 TCTTTAGTTAACATTAATCAGATTTGCATCTTGTATGCAATTCTATGTGTTTAATATTGTTAGCA
* *
33721 ATGAGGCCTGCTGGTTTTATCCTACTGTTT
196 ATGAGGCCTGCTGGTTTTATCATACTATTT
33751 TGCATCCTGATGATGATGAATATGCATTGTTAAAAGTA
1 TGCATCCTGATGATGATGAATATGCATTGTTAAAAGTA
33789 ATGCCAGATC
Statistics
Matches: 256, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
224 99 0.39
225 157 0.61
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (225 bp):
TGCATCCTGATGATGATGAATATGCATTGTTAAAAGTAGTGACTGATTGATTAATGATAGGTCGA
CGATAAATACATGATATTGAGGGATGCAAAAGGAAATTTTTTTATATTGTTCATCTTTGAAAACA
TCTTTAGTTAACATTAATCAGATTTGCATCTTGTATGCAATTCTATGTGTTTAATATTGTTAGCA
ATGAGGCCTGCTGGTTTTATCATACTATTT
Found at i:34996 original size:40 final size:41
Alignment explanation
Indices: 34952--35041 Score: 164
Period size: 40 Copynumber: 2.2 Consensus size: 41
34942 TTAATGTTCA
34952 TTTATGTTCGTTTTTTAGCTAAATAAACGAGTATGA-ATTT
1 TTTATGTTCGTTTTTTAGCTAAATAAACGAGTATGATATTT
*
34992 TTTATGTTCGTTTTTTAGCTAAATAAACGAGTATGATTTTT
1 TTTATGTTCGTTTTTTAGCTAAATAAACGAGTATGATATTT
35033 TTTATGTTC
1 TTTATGTTC
35042 ATTTAATAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 36 0.75
41 12 0.25
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (41 bp):
TTTATGTTCGTTTTTTAGCTAAATAAACGAGTATGATATTT
Found at i:38610 original size:44 final size:44
Alignment explanation
Indices: 38555--38640 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
38545 GAAAGTAACC
*
38555 TCAAAGATTCTTTCTTCACAGCTTGTTTTGGATCATTTGAAGAA
1 TCAAAGATTCTTTCTTCACAGCTTGTTTTGGATCATTGGAAGAA
* *
38599 TCAAAGATTCTTTCTTTACAGCTTGTTTTGGGTCATTGGAAG
1 TCAAAGATTCTTTCTTCACAGCTTGTTTTGGATCATTGGAAG
38641 GGAGTCAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (44 bp):
TCAAAGATTCTTTCTTCACAGCTTGTTTTGGATCATTGGAAGAA
Found at i:40185 original size:11 final size:11
Alignment explanation
Indices: 40164--40192 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40154 CTCGTCTCGG
40164 GTCGT-GTCGT
1 GTCGTGGTCGT
40174 GTCGTGGTCGT
1 GTCGTGGTCGT
40185 GTCGTGGT
1 GTCGTGGT
40193 AATACGTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.00, C:0.17, G:0.45, T:0.38
Consensus pattern (11 bp):
GTCGTGGTCGT
Found at i:40328 original size:41 final size:40
Alignment explanation
Indices: 40271--40424 Score: 188
Period size: 41 Copynumber: 3.8 Consensus size: 40
40261 TTTTTTTTTA
*
40271 ACTATCGCAA-CGAATTTGGAAAATCGCAACGACAATTGTAG
1 ACTATCGCAACCGAA-ATGGAAAATCGCAACGAC-ATTGTAG
* *
40312 ACTATCGCAA-CGAATTTAGAAAATCGCAACGACATTGTAG
1 ACTATCGCAACCGAA-ATGGAAAATCGCAACGACATTGTAG
* *
40352 ACTATCGCAACGCGAAATGGAAAATCGCAACGAGATTTTCA-
1 ACTATCGCAAC-CGAAATGGAAAATCGCAACGACATTGT-AG
40393 ACTATCGCAACGCGAAATGGAAAATCGCAACG
1 ACTATCGCAAC-CGAAATGGAAAATCGCAACG
40425 CGAAATAGAA
Statistics
Matches: 105, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
40 17 0.16
41 83 0.79
42 5 0.05
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (40 bp):
ACTATCGCAACCGAAATGGAAAATCGCAACGACATTGTAG
Found at i:40380 original size:20 final size:20
Alignment explanation
Indices: 40355--40447 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
40345 ATTGTAGACT
40355 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
40375 ATCGCAACGAGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
40396 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
40416 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
*
40436 ATCGTAACGCGA
1 ATCGCAACGCGA
40448 TTTTCAACAA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:40425 original size:61 final size:61
Alignment explanation
Indices: 40355--40469 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
40345 ATTGTAGACT
* *
40355 ATCGCAACGCGAAATGGAAAATCGCAACGAGATTTTCAAC-TATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAAATCGCAACGAGATTTTCAACAAAT-GCAACGCGAAATGGAAA
* *
40416 ATCGCAACGCGAAATAGAAAATCGTAACGCGATTTTCAACAAATGCAACGCGAA
1 ATCGCAACGCGAAATAGAAAATCGCAACGAGATTTTCAACAAATGCAACGCGAA
40470 TTTGCGATAG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
61 47 0.96
62 2 0.04
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.17
Consensus pattern (61 bp):
ATCGCAACGCGAAATAGAAAATCGCAACGAGATTTTCAACAAATGCAACGCGAAATGGAAA
Found at i:40509 original size:19 final size:19
Alignment explanation
Indices: 40485--40528 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
40475 GATAGTGGAA
40485 ATCGCAATGCGAATTAAAG
1 ATCGCAATGCGAATTAAAG
40504 ATCGCAATGCGAATTAAAG
1 ATCGCAATGCGAATTAAAG
40523 ATCGCA
1 ATCGCA
40529 TTACGATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (19 bp):
ATCGCAATGCGAATTAAAG
Found at i:49976 original size:14 final size:12
Alignment explanation
Indices: 49939--49971 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
49929 CTTATTAAAA
*
49939 TCCTTCTCTCTC
1 TCCTTCTCTTTC
49951 TCCTTCTCTTTC
1 TCCTTCTCTTTC
49963 TCCTTCTCT
1 TCCTTCTCT
49972 GTTTCCCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (12 bp):
TCCTTCTCTTTC
Found at i:59588 original size:11 final size:11
Alignment explanation
Indices: 59572--59603 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
59562 TTTATCATTA
59572 TTATTTTTTTC
1 TTATTTTTTTC
59583 TTATTTTTTTC
1 TTATTTTTTTC
*
59594 CTATTTTTTT
1 TTATTTTTTT
59604 ATCATTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (11 bp):
TTATTTTTTTC
Found at i:59881 original size:30 final size:30
Alignment explanation
Indices: 59842--59937 Score: 111
Period size: 30 Copynumber: 3.0 Consensus size: 30
59832 CGCAACATTA
59842 ATTACCGATATAGGTAAACACAACTATCGT
1 ATTACCGATATAGGTAAACACAACTATCGT
*
59872 ATTAGCGATATAGGTAAACACAACTATCGCAACGCT
1 ATTACCGATATAGGTAAACACAACTAT-----CG-T
*
59908 AATTACCTATATAGGTAAACACAACTATCG
1 -ATTACCGATATAGGTAAACACAACTATCG
59938 CAATGCGAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
30 26 0.46
32 2 0.04
35 2 0.04
36 1 0.02
37 25 0.45
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (30 bp):
ATTACCGATATAGGTAAACACAACTATCGT
Found at i:59960 original size:20 final size:20
Alignment explanation
Indices: 59935--59990 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
59925 AACACAACTA
*
59935 TCGCAATGCGAATTTCATTT
1 TCGCAACGCGAATTTCATTT
*
59955 TCGCAACGCGGATTTCATTT
1 TCGCAACGCGAATTTCATTT
*
59975 TTGCAACGCGAATTTC
1 TCGCAACGCGAATTTC
59991 GCAAATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (20 bp):
TCGCAACGCGAATTTCATTT
Found at i:60991 original size:30 final size:30
Alignment explanation
Indices: 60955--61014 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
60945 TATAAACCGA
60955 CCATTGTGCATGTTTGTGATAGATTTATAG
1 CCATTGTGCATGTTTGTGATAGATTTATAG
60985 CCATTGTGCATGTTTGTGATAGATTTATAG
1 CCATTGTGCATGTTTGTGATAGATTTATAG
61015 TCAATATTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (30 bp):
CCATTGTGCATGTTTGTGATAGATTTATAG
Found at i:62004 original size:18 final size:18
Alignment explanation
Indices: 61978--62023 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
61968 ACCGGTCACA
61978 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
61996 ACCCTACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
62014 ACCCGACCCG
1 ACCCGACCCG
62024 TTGACCGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.17, C:0.52, G:0.17, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:62016 original size:13 final size:13
Alignment explanation
Indices: 62000--62025 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61990 CCGTTGACCC
62000 TACCCGACCCGTT
1 TACCCGACCCGTT
62013 TACCCGACCCGTT
1 TACCCGACCCGTT
62026 GACCGTTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.46, G:0.15, T:0.23
Consensus pattern (13 bp):
TACCCGACCCGTT
Found at i:64629 original size:12 final size:12
Alignment explanation
Indices: 64614--64643 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
64604 TCTAATCTGG
64614 ATTCTGTTTTGA
1 ATTCTGTTTTGA
64626 ATTCTGTTTTGA
1 ATTCTGTTTTGA
*
64638 TTTCTG
1 ATTCTG
64644 ATATATTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (12 bp):
ATTCTGTTTTGA
Found at i:66530 original size:6 final size:6
Alignment explanation
Indices: 66511--66544 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
66501 TTAAACATAC
* *
66511 ATTCAT ATTTAT ATCCAT ATTCAT ATTCAT ATTC
1 ATTCAT ATTCAT ATTCAT ATTCAT ATTCAT ATTC
66545 GAATCTAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTCAT
Found at i:69828 original size:34 final size:34
Alignment explanation
Indices: 69790--69859 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
69780 GACCAATATA
69790 TAAATATTTCAAAATATTGGATTTAATAACTTAT
1 TAAATATTTCAAAATATTGGATTTAATAACTTAT
69824 TAAATATTTCAAAATATTGGATTTAATAACTTAT
1 TAAATATTTCAAAATATTGGATTTAATAACTTAT
69858 TA
1 TA
69860 CAAACTTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (34 bp):
TAAATATTTCAAAATATTGGATTTAATAACTTAT
Found at i:77257 original size:21 final size:21
Alignment explanation
Indices: 77231--77275 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
77221 CCGGAAATGT
*
77231 TAAAAATATTAATATTTTAAG
1 TAAAAATAATAATATTTTAAG
*
77252 TAAAAATAATAATATTTTAGG
1 TAAAAATAATAATATTTTAAG
77273 TAA
1 TAA
77276 TTTTTTACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAG
Found at i:81468 original size:4 final size:4
Alignment explanation
Indices: 81459--81495 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
81449 CCCACAGATC
* *
81459 TTAT TTAT TTAT TTAT TTAC TTAT TTAC TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
81496 AAATTCATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (4 bp):
TTAT
Found at i:82663 original size:24 final size:24
Alignment explanation
Indices: 82604--82674 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
82594 TTGTATAAAT
* *
82604 TGCACCGAAGTACCGCGTAAAAAG
1 TGCACCGAAGTGCCGCGTAGAAAG
*
82628 TGCACTGAAGTGCCGCGTAGAAAG
1 TGCACCGAAGTGCCGCGTAGAAAG
* *
82652 TGCACCGAAGTGCCACATAGAAA
1 TGCACCGAAGTGCCGCGTAGAAA
82675 TATCCCAAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.35, C:0.24, G:0.27, T:0.14
Consensus pattern (24 bp):
TGCACCGAAGTGCCGCGTAGAAAG
Found at i:82724 original size:23 final size:23
Alignment explanation
Indices: 82664--82725 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
82654 CACCGAAGTG
*
82664 CCACATAGAAATATCCCAAAGGA
1 CCACATAGAAATGTCCCAAAGGA
* * *
82687 CCACATAGTATTGTCCCGAAGGA
1 CCACATAGAAATGTCCCAAAGGA
* *
82710 CCGCGTAGAAATGTCC
1 CCACATAGAAATGTCC
82726 AGAAAAACCA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (23 bp):
CCACATAGAAATGTCCCAAAGGA
Found at i:85142 original size:21 final size:21
Alignment explanation
Indices: 85113--85157 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
85103 GATTTCTGGG
* *
85113 CAAGAGGAATCGGTACCCATT
1 CAAGAGGAACCGATACCCATT
* *
85134 CAAGGGGAACCGATACCCCTT
1 CAAGAGGAACCGATACCCATT
85155 CAA
1 CAA
85158 ACGACAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGAGGAACCGATACCCATT
Found at i:85760 original size:18 final size:18
Alignment explanation
Indices: 85737--85771 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
85727 CTAGGAGATT
85737 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
85755 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
85772 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:85857 original size:21 final size:22
Alignment explanation
Indices: 85828--85871 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
85818 GTTGTATGAT
85828 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
85849 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
85871 A
1 A
85872 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:86263 original size:20 final size:19
Alignment explanation
Indices: 86219--86265 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
86209 ACACGATATG
*
86219 TTATGT-ATGTTAAAGGAA
1 TTATGTGATGTGAAAGGAA
*
86237 TTATGTGATGTGAAAGTAA
1 TTATGTGATGTGAAAGGAA
86256 TCTATGTGAT
1 T-TATGTGAT
86266 TATATGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.24
19 11 0.44
20 8 0.32
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.40
Consensus pattern (19 bp):
TTATGTGATGTGAAAGGAA
Found at i:86679 original size:149 final size:149
Alignment explanation
Indices: 86499--86802 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
86489 GAGTCGAGGG
86499 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
* *
86564 ACTTGATCCATAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
86629 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
86648 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
86713 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
86778 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
86797 TCTACG
1 TCTACG
86803 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCATAGCATATGTATATGATTCTTAAAGAATTCTACGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:86825 original size:23 final size:23
Alignment explanation
Indices: 86781--86825 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
86771 ATCATTATAT
*
86781 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
86804 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
86826 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:89450 original size:16 final size:17
Alignment explanation
Indices: 89401--89462 Score: 79
Period size: 17 Copynumber: 3.4 Consensus size: 17
89391 GACATAATAC
*
89401 TTAAATAATATTATTTT
1 TTAAAAAATATTATTTT
89418 TTAAAATTAATATTATTTTTT
1 TTAAAA--AATATTA--TTTT
89439 TTAAAAAATATTATTTT
1 TTAAAAAATATTATTTT
89456 TTAAAAA
1 TTAAAAA
89463 TAATACTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
17 16 0.40
19 14 0.35
21 10 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAAAAAATATTATTTT
Found at i:89463 original size:16 final size:18
Alignment explanation
Indices: 89403--89467 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 18
89393 CATAATACTT
89403 AAATAATATTATTTTTTA
1 AAATAATATTATTTTTTA
89421 AAATTAATATTATTTTTTTTA
1 AAA-TAATATTA--TTTTTTA
89442 AAA-AATATTATTTTTTAA
1 AAATAATATTATTTTTT-A
89460 AAATAATA
1 AAATAATA
89468 CTTTTATCAC
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.14
18 7 0.17
19 19 0.45
21 10 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AAATAATATTATTTTTTA
Found at i:89472 original size:17 final size:17
Alignment explanation
Indices: 89401--89472 Score: 56
Period size: 16 Copynumber: 4.1 Consensus size: 17
89391 GACATAATAC
* *
89401 TTAAATAATATTATTTT
1 TTAAAAAATAATATTTT
*
89418 TTAAAATTAATATTATTTTTT
1 TTAAAA--AATA--ATATTTT
*
89439 TTAAAAAATATTATTTT
1 TTAAAAAATAATATTTT
*
89456 TT-AAAAATAATACTTT
1 TTAAAAAATAATATTTT
89472 T
1 T
89473 ATCACGTAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
16 13 0.30
17 12 0.27
19 8 0.18
21 11 0.25
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAAAATAATATTTT
Found at i:89564 original size:91 final size:92
Alignment explanation
Indices: 89439--89608 Score: 279
Period size: 91 Copynumber: 1.9 Consensus size: 92
89429 ATTATTTTTT
** *
89439 TTAAAAAATATTATTTTTTAAAAATAATACTTTTATCACGTAAAATAAAAATATATCATCTAAAA
1 TTAAAAAATATTATTTTAAAAAAACAATACTTTTATCACGTAAAATAAAAATATATCATCTAAAA
89504 AATAAAGACATATTAGAGACATAATAC
66 AATAAAGACATATTAGAGACATAATAC
* * *
89531 TTAAATAATATTA-TTTAAAAAAACAATACTTTTATCAGGTAAAATCAAAATATATCATCTAAAA
1 TTAAAAAATATTATTTTAAAAAAACAATACTTTTATCACGTAAAATAAAAATATATCATCTAAAA
89595 AATAAAGACATATT
66 AATAAAGACATATT
89609 TAACTAATTA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 60 0.83
92 12 0.17
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.34
Consensus pattern (92 bp):
TTAAAAAATATTATTTTAAAAAAACAATACTTTTATCACGTAAAATAAAAATATATCATCTAAAA
AATAAAGACATATTAGAGACATAATAC
Found at i:94303 original size:21 final size:21
Alignment explanation
Indices: 94273--94322 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
94263 GTTCGGGTCA
94273 GGTCGGGTTTGAATAAAATTG
1 GGTCGGGTTTGAATAAAATTG
*
94294 GGTTGGGTTTGAATAAAATTG
1 GGTCGGGTTTGAATAAAATTG
94315 GGTCGGGT
1 GGTCGGGT
94323 ATCGGGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.04, G:0.38, T:0.34
Consensus pattern (21 bp):
GGTCGGGTTTGAATAAAATTG
Found at i:94428 original size:34 final size:33
Alignment explanation
Indices: 94388--94491 Score: 142
Period size: 34 Copynumber: 3.2 Consensus size: 33
94378 CCGATTATAC
*
94388 ATATATAATATTTTTTTTATTTTTTATATTAATT
1 ATATATAATA-TTTTTATATTTTTTATATTAATT
94422 ATATAT-ATAATATTTTATATTTTTTATATTAATT
1 ATATATAAT-AT-TTTTATATTTTTTATATTAATT
94456 ATATATAATA-TTTTATA-TTTTTATATTAATT
1 ATATATAATATTTTTATATTTTTTATATTAATT
*
94487 GTATA
1 ATATA
94492 ATACAAACCC
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
31 18 0.28
32 7 0.11
33 3 0.05
34 35 0.54
35 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
ATATATAATATTTTTATATTTTTTATATTAATT
Found at i:94437 original size:25 final size:28
Alignment explanation
Indices: 94409--94474 Score: 75
Period size: 32 Copynumber: 2.3 Consensus size: 28
94399 TTTTTTTATT
94409 TTTTATATTA-ATT-A-TATATATAATA
1 TTTTATATTATATTAATTATATATAATA
94434 TTTTATATTTTTTATATTAATTATATATAATA
1 TTTTATA----TTATATTAATTATATATAATA
94466 TTTTATATT
1 TTTTATATT
94475 TTTATATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
25 7 0.21
28 2 0.06
29 3 0.09
30 3 0.09
31 1 0.03
32 18 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTATATTATATTAATTATATATAATA
Found at i:94908 original size:22 final size:22
Alignment explanation
Indices: 94883--94925 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
94873 ATTGCAATTT
94883 ATGAAATATAAATATTTTTTTG
1 ATGAAATATAAATATTTTTTTG
*
94905 ATGAAATCTAAATATTTTTTT
1 ATGAAATATAAATATTTTTTT
94926 AATCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (22 bp):
ATGAAATATAAATATTTTTTTG
Found at i:95341 original size:23 final size:23
Alignment explanation
Indices: 95315--95358 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
95305 TTGTCTAGCA
*
95315 TTTGTGAATATATTTATTTAACG
1 TTTGTGAACATATTTATTTAACG
* *
95338 TTTGTTAACATGTTTATTTAA
1 TTTGTGAACATATTTATTTAA
95359 GGTTCGTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.55
Consensus pattern (23 bp):
TTTGTGAACATATTTATTTAACG
Found at i:95576 original size:12 final size:12
Alignment explanation
Indices: 95559--95603 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
95549 GGATAATCAA
95559 ATAAACGAGTCG
1 ATAAACGAGTCG
*
95571 ATAAACGAG-CTT
1 ATAAACGAGTC-G
*
95583 ATAAACGATTCG
1 ATAAACGAGTCG
95595 ATAAACGAG
1 ATAAACGAG
95604 CTAATAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (12 bp):
ATAAACGAGTCG
Found at i:95586 original size:24 final size:24
Alignment explanation
Indices: 95558--95612 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
95548 AGGATAATCA
95558 AATAAACGAGTCGATAAACGAGCT
1 AATAAACGAGTCGATAAACGAGCT
* *
95582 TATAAACGATTCGATAAACGAGCT
1 AATAAACGAGTCGATAAACGAGCT
95606 AATAAAC
1 AATAAAC
95613 AAACTTGTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.20
Consensus pattern (24 bp):
AATAAACGAGTCGATAAACGAGCT
Found at i:96695 original size:19 final size:19
Alignment explanation
Indices: 96663--96705 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 19
96653 AGGTTTTTTG
*
96663 TTTTTTAATTATAATATTAAT
1 TTTTTTAA-TATAA-AATAAT
96684 TTTTTTAA-ATAAAATAAT
1 TTTTTTAATATAAAATAAT
96702 TTTT
1 TTTT
96706 AAAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 4 0.19
21 8 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTTAATATAAAATAAT
Found at i:101120 original size:38 final size:38
Alignment explanation
Indices: 101042--101120 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
101032 TTTTTATATT
*
101042 TTTAATTTTGTAAAAAAAAGTTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAAGTTATATAAATATTATCAA
* * *
101080 TTTAATTTTTTAAAGAAAA-TTATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAAGTTATATAAATATTAT-CAA
101118 TTT
1 TTT
101121 GTAATATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 14 0.39
38 22 0.61
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (38 bp):
TTTAATTTTGTAAAAAAAAGTTATATAAATATTATCAA
Found at i:101302 original size:20 final size:20
Alignment explanation
Indices: 101266--101303 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
101256 ATCCTATTCC
**
101266 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
101286 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
101304 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:101830 original size:20 final size:20
Alignment explanation
Indices: 101805--101845 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
101795 AGAGCAAAGA
*
101805 AAAGCGTGTCACAAGGATAG
1 AAAGCGAGTCACAAGGATAG
101825 AAAGCGAGTCACAAGGATAG
1 AAAGCGAGTCACAAGGATAG
101845 A
1 A
101846 GATTCTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.29, T:0.12
Consensus pattern (20 bp):
AAAGCGAGTCACAAGGATAG
Found at i:105409 original size:21 final size:19
Alignment explanation
Indices: 105375--105427 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 19
105365 TTTGAGAATT
105375 TATTTTTAAAAAATAAAAA
1 TATTTTTAAAAAATAAAAA
*
105394 TATTTTTATTAAAAATAAATA
1 TATTTTTA--AAAAATAAAAA
**
105415 TATAGTTAAAAAA
1 TATTTTTAAAAAA
105428 ACTTTTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 13 0.45
21 16 0.55
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TATTTTTAAAAAATAAAAA
Found at i:107819 original size:31 final size:31
Alignment explanation
Indices: 107780--107869 Score: 137
Period size: 31 Copynumber: 2.9 Consensus size: 31
107770 AGAGTCGAGG
107780 GTTACCTATGTCTTTCGAGACATATGGACA-
1 GTTACCTATGTCTTTCGAGACATATGGACAT
* *
107810 GTTTACCTATGTCTTTCGGGACATATAGACAT
1 G-TTACCTATGTCTTTCGAGACATATGGACAT
*
107842 GTTACCTATGTCATTCGAGACATATGGA
1 GTTACCTATGTCTTTCGAGACATATGGA
107870 TAGTGGTCCT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.02
31 51 0.96
32 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTACCTATGTCTTTCGAGACATATGGACAT
Found at i:113941 original size:2 final size:2
Alignment explanation
Indices: 113870--113923 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
113860 TGTGTGAGTT
113870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
113912 TA TA TA TA TA TA
1 TA TA TA TA TA TA
113924 GTTTTTTAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:114079 original size:2 final size:2
Alignment explanation
Indices: 114072--114097 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
114062 CCGTTGCTTT
114072 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
114098 AGTTCTTCTA
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):
TA
Found at i:114574 original size:34 final size:34
Alignment explanation
Indices: 114531--114632 Score: 186
Period size: 34 Copynumber: 3.0 Consensus size: 34
114521 ATAAGATCAC
* *
114531 GTTGCATTGTGGTTCCTAGGGTACTTTTGCTGCT
1 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
114565 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
1 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
114599 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
1 GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
114633 TTTGAGCTTT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.07, C:0.18, G:0.29, T:0.46
Consensus pattern (34 bp):
GTTGCATTGTGGTTCTTCGGGTACTTTTGCTGCT
Found at i:120382 original size:66 final size:65
Alignment explanation
Indices: 120276--120473 Score: 333
Period size: 66 Copynumber: 3.0 Consensus size: 65
120266 ATAGTCAAAT
*
120276 TATCCAGATTAACCTTCCACCCCGAAGAGCCCTCATAGGTCCGAAGAATACCCTTAGAACATTGA
1 TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTT-GAACATTGA
120341 G
65 G
*
120342 TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTTGGAGCATTGA
1 TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTT-GAACATTGA
120407 G
65 G
* *
120408 TATCCAGATTAACCTTTCACCCCAAAGAGCCCTCATAGGTCGGAAGAATACCCTTGAAACATTGA
1 TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTTG-AACATTGA
120473 G
65 G
120474 CTTCGTACGA
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
65 1 0.01
66 124 0.99
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (65 bp):
TATCCAGATTAACCTTCCACCCCAAAGAGCCCTCATAGGTCCGAAGAATACCCTTGAACATTGAG
Found at i:124405 original size:24 final size:24
Alignment explanation
Indices: 124359--124406 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
124349 AAACGTTAAT
* *
124359 TGAATATATTCGTCACAACTAAAA
1 TGAATATATTCATCAAAACTAAAA
* *
124383 TGAATATATTCATGAAAATTAAAA
1 TGAATATATTCATCAAAACTAAAA
124407 AAACAATCGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (24 bp):
TGAATATATTCATCAAAACTAAAA
Found at i:124527 original size:22 final size:20
Alignment explanation
Indices: 124494--124533 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
124484 AAATTTAAAT
124494 AAATATAAAAATAAAAATAA
1 AAATATAAAAATAAAAATAA
124514 AAATATAAACAAATAAAAAT
1 AAATAT-AA-AAATAAAAAT
124534 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATATAAAAATAAAAATAA
Found at i:125427 original size:228 final size:227
Alignment explanation
Indices: 125019--126157 Score: 1273
Period size: 228 Copynumber: 5.0 Consensus size: 227
125009 TTAAAAGCTG
* * * * ** * * * * *
125019 CCACCACGGAGTCGAAGGACCAAGTGCAAAGTTGATTCCTTCTGGATGTTGTAGTCTGCCAGGGT
1 CCACCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCTGCCAAGGT
* * * * * * * * * *
125084 CCTCCCATCTTCAAGCTGCTTCCCAGCAAAGATCAACCTCTGCTGATCCGG-GGGAATTCCTTCC
66 GCGCCCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCTGGAGGG-ATACCCTCC
* * * * * * *
125148 TTATCCTGAATCTTGGCCTTGACATTATCAATCGTGTCCGAGCTCTCAACCTCTAGGGTGATAGT
130 TTATCCTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGT
* *
125213 TTTCCCAGTGAGGGTCTTCACAAAAATTTGCATC
195 TTT-CCAGTGAGGGTCTTAACAAAAATTTGCATA
*
125247 CCACCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCAGCCAAGGT
1 CCACCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCTGCCAAGGT
* * * *
125312 GCGCCCATCCTCAAGTTGCTTACCTGCAAAAATCAACCTCTGCTGGTCTGGCGGGATACCCTCCT
66 GCGCCCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCTGGAGGGATACCCTCCT
* * * * *
125377 TGTCCTGAATCTTGGCCTTGACATTATCTATTGTGTCGGAACTTTCAACCTCCAAGGTGATGGTC
131 TATCCTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGT-
* * * *
125442 TTTCCAGTAAGTGTCTTCACAAAAATCTGCATA
195 TTTCCAGTGAGGGTCTTAACAAAAATTTGCATA
*
125475 CCACCACGAAGACGGAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCTGCCAAGGT
1 CCACCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCTGCCAAGGT
* * * * *
125540 GCGCCCATCTTCCAGTTGCTTCCCAGCAAAGATCAGCCTCTGTTGGTCTGGGGGGATACCCTCCT
66 GCGCCCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCTGGAGGGATACCCTCCT
* * *
125605 TGTCCTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAGCTTTCAACTTCCAAGGTGATGGTC
131 TATCCTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGT-
* * * * *
125670 TTCCCAGTAAGTGTCTTAACAAATATCTGCATA
195 TTTCCAGTGAGGGTCTTAACAAAAATTTGCATA
* *
125703 CCACCTCGAAGACGGAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCTGCCAAGGT
1 CCACCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCTGCCAAGGT
* *
125768 GCGCCCATCCTCCAGTTGCTTACCAGCAAAGATCAGCCTCTGTTGGTCTGGAGGGATACCCTCCT
66 GCGCCCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCTGGAGGGATACCCTCCT
* * * * * * *
125833 TATCCTGAATCTTGGCCTTGACATTGTCAATGGTATCTGAACTCTCCACCTCCAATGTAATGGTC
131 TATCCTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGT-
* *
125898 TTTCCGGTGAGGGTCTTAACAAAGATTTGCATA
195 TTTCCAGTGAGGGTCTTAACAAAAATTTGCATA
* * * * * * * * *
125931 CCACCCCTCAA-TCGAAGGACCAAGTGGAGTGTGGATTCCTTCTGGATGTTATAATCAG-CAAGG
1 CCACCAC-GAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCTGCCAA-G
* * * * * *
125994 GTCCGGCCATCCTCCAA-CTGTTTACCAGCAAAGAT-AAGCCTCTGTTGGTCAGGAGGGATTCCC
64 GTGCGCCCATCCT-CAAGTTGCTTACCAGCAAAGATCAA-CCTCTGTTGGTCTGGAGGGATACCC
* * * * * * *
126057 TCCTTATCTTGGATCTTGGCCTTTACATTGTCGATGGTATCAGAACTTTCCACCT-CAAGGGTGA
127 TCCTTATCCTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAA-GGTGA
* * *
126121 TGGTCTTGCCAGTGAGGGTCTTGACGAAAATTTGCAT
191 TGGT-TTTCCAGTGAGGGTCTTAACAAAAATTTGCAT
126158 CTATTGTGAG
Statistics
Matches: 798, Mismatches: 106, Indels: 14
0.87 0.12 0.02
Matches are distributed among these distances:
227 7 0.01
228 781 0.98
229 10 0.01
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (227 bp):
CCACCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCTGCCAAGGT
GCGCCCATCCTCAAGTTGCTTACCAGCAAAGATCAACCTCTGTTGGTCTGGAGGGATACCCTCCT
TATCCTGAATCTTGGCCTTGACATTGTCAATCGTGTCAGAACTTTCAACCTCCAAGGTGATGGTT
TTCCAGTGAGGGTCTTAACAAAAATTTGCATA
Found at i:125886 original size:456 final size:456
Alignment explanation
Indices: 125055--126157 Score: 1411
Period size: 456 Copynumber: 2.4 Consensus size: 456
125045 CAAAGTTGAT
* * * * *
125055 TCCTTCTGGATGTTGTAGTCTGCCAGGGTCCTCCCATCTTCAAGCTGCTTCCCAGCAAAGATCAA
1 TCCTTCTGGATGTTATAGTCTGCCAAGGTCCGCCCATCTTCCAGCTGCTTCCCAGCAAAGATCAG
* * * * * *
125120 CCTCTGCTGATCCGGGGGAATTCCTTCCTTATCCTGAATCTTGGCCTTGACATTATCAATCGTGT
66 CCTCTGTTGGTCAGGGGGGATTCCCTCCTTATCCTGAATCTTGGCCTTGACATTGTCAATCGTGT
* * * * * * * * *
125185 CCGAGCTCTCAACCTCTAGGGTGATAGTTTTCCCAGTGAGGGTCTTCACAAAAATTTGCATCCCA
131 CAGAGCTTTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCTTAACAAAAATCTGCATACCA
125250 CCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCAGCCAAGGTGCG
196 CCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCAGCCAAGGTGCG
* * *
125315 CCCATCCTCAAGTTGCTTACCTGCAAAAATCAACCTCTGCTGGTCTGGCGGGATACCCTCCTTGT
261 CCCATCCTCAAGTTGCTTACCAGCAAAAATCAACCTCTGCTGGTCTGGAGGGATACCCTCCTTAT
* * * * *
125380 CCTGAATCTTGGCCTTGACATTATCTATTGTGTCGGAACTTTCAACCTCCAAGGTGATGGTCTTT
326 CCTGAATCTTGGCCTTGACATTATCAATGGTATCGGAACTCTCAACCTCCAAGGTAATGGTCTTT
* * * *
125445 CCAGTAAGTGTCTTCACAAAAATCTGCATACCACCAC-GAAGACGGAGCACCAAGTGGAGGGTGG
391 CCAGTAAGGGTCTTAACAAAAATCTGCATACCACCACTCAA-ACGAAGCACCAAGTGGAGGGTGG
125509 AC
455 AC
* * *
125511 TCCTTTTGGATGTTATAGTCTGCCAAGGTGCGCCCATCTTCCAGTTGCTTCCCAGCAAAGATCAG
1 TCCTTCTGGATGTTATAGTCTGCCAAGGTCCGCCCATCTTCCAGCTGCTTCCCAGCAAAGATCAG
* * *
125576 CCTCTGTTGGTCTGGGGGGATACCCTCCTTGTCCTGAATCTTGGCCTTGACATTGTCAATCGTGT
66 CCTCTGTTGGTCAGGGGGGATTCCCTCCTTATCCTGAATCTTGGCCTTGACATTGTCAATCGTGT
* * * *
125641 CAGAGCTTTCAACTTCCAAGGTGATGGTCTTCCCAGTAAGTGTCTTAACAAATATCTGCATACCA
131 CAGAGCTTTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCTTAACAAAAATCTGCATACCA
* * *
125706 CCTCGAAGACGGAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCTGCCAAGGTGCG
196 CCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCAGCCAAGGTGCG
* * * *
125771 CCCATCCTCCAGTTGCTTACCAGCAAAGATCAGCCTCTGTTGGTCTGGAGGGATACCCTCCTTAT
261 CCCATCCTCAAGTTGCTTACCAGCAAAAATCAACCTCTGCTGGTCTGGAGGGATACCCTCCTTAT
* * * *
125836 CCTGAATCTTGGCCTTGACATTGTCAATGGTATCTGAACTCTCCACCTCCAATGTAATGGTCTTT
326 CCTGAATCTTGGCCTTGACATTATCAATGGTATCGGAACTCTCAACCTCCAAGGTAATGGTCTTT
* * * * * * * *
125901 CCGGTGAGGGTCTTAACAAAGATTTGCATACCACCCCTCAATCGAAGGACCAAGTGGAGTGTGGA
391 CCAGTAAGGGTCTTAACAAAAATCTGCATACCACCACTCAAACGAAGCACCAAGTGGAGGGTGGA
*
125966 T
456 C
* * * * * * * *
125967 TCCTTCTGGATGTTATAATCAG-CAAGGGTCCGGCCATCCTCCAACTGTTTACCAGCAAAGATAA
1 TCCTTCTGGATGTTATAGTCTGCCAA-GGTCCGCCCATCTTCCAGCTGCTTCCCAGCAAAGATCA
* * * * * * *
126031 GCCTCTGTTGGTCAGGAGGGATTCCCTCCTTATCTTGGATCTTGGCCTTTACATTGTCGATGGTA
65 GCCTCTGTTGGTCAGGGGGGATTCCCTCCTTATCCTGAATCTTGGCCTTGACATTGTCAATCGTG
* * * * * *
126096 TCAGAACTTTCCACCT-CAAGGGTGATGGTCTTGCCAGTGAGGGTCTTGACGAAAATTTGCAT
130 TCAGAGCTTTCAACCTCCAA-GGTGATGGTCTTCCCAGTGAGGGTCTTAACAAAAATCTGCAT
126158 CTATTGTGAG
Statistics
Matches: 552, Mismatches: 92, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
455 6 0.01
456 544 0.99
457 2 0.00
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (456 bp):
TCCTTCTGGATGTTATAGTCTGCCAAGGTCCGCCCATCTTCCAGCTGCTTCCCAGCAAAGATCAG
CCTCTGTTGGTCAGGGGGGATTCCCTCCTTATCCTGAATCTTGGCCTTGACATTGTCAATCGTGT
CAGAGCTTTCAACCTCCAAGGTGATGGTCTTCCCAGTGAGGGTCTTAACAAAAATCTGCATACCA
CCACGAAGACGAAGCACCAAGTGGAGGGTGGACTCCTTTTGGATGTTATAGTCAGCCAAGGTGCG
CCCATCCTCAAGTTGCTTACCAGCAAAAATCAACCTCTGCTGGTCTGGAGGGATACCCTCCTTAT
CCTGAATCTTGGCCTTGACATTATCAATGGTATCGGAACTCTCAACCTCCAAGGTAATGGTCTTT
CCAGTAAGGGTCTTAACAAAAATCTGCATACCACCACTCAAACGAAGCACCAAGTGGAGGGTGGA
C
Found at i:127161 original size:60 final size:60
Alignment explanation
Indices: 127068--127189 Score: 163
Period size: 60 Copynumber: 2.0 Consensus size: 60
127058 TTTTCGTTGG
* *
127068 ATAAACTATCAAAATGGTCTCTTCATTTTCATAAACATTCACTTTTAGCCACTTAATTAT
1 ATAAACTATCAAAACGGTCTCTTCAGTTTCATAAACATTCACTTTTAGCCACTTAATTAT
** * * * * *
127128 ATAAACTATCAAAACGGTCTCTTTGGTTTCATAAATATTTATTTTTGGTCACTTAATTAT
1 ATAAACTATCAAAACGGTCTCTTCAGTTTCATAAACATTCACTTTTAGCCACTTAATTAT
127188 AT
1 AT
127190 TAAATATTTC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (60 bp):
ATAAACTATCAAAACGGTCTCTTCAGTTTCATAAACATTCACTTTTAGCCACTTAATTAT
Found at i:134078 original size:18 final size:18
Alignment explanation
Indices: 134002--134079 Score: 50
Period size: 18 Copynumber: 4.1 Consensus size: 18
133992 GACTCCCATG
*
134002 TTAAATTAATTTTTAAAT
1 TTAAATTAATTATTAAAT
* *
134020 TTAAAATTATTTATATCGATAT
1 TT-AAATTAATTAT-T--AAAT
* * *
134042 TCAAATTAA-GATTTGAAT
1 TTAAATTAATTA-TTAAAT
134060 TTAAATTAATTATTAAAT
1 TTAAATTAATTATTAAAT
134078 TT
1 TT
134080 TAAAATATTT
Statistics
Matches: 43, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
18 19 0.44
19 10 0.23
20 3 0.07
21 7 0.16
22 4 0.09
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (18 bp):
TTAAATTAATTATTAAAT
Found at i:138666 original size:57 final size:57
Alignment explanation
Indices: 138605--138835 Score: 232
Period size: 57 Copynumber: 3.9 Consensus size: 57
138595 GAGGAATAGG
* * * *
138605 AGGAGGCAGTTGTGCAGCACGAGAAACAGGAGGCGATGGTGCAGCATGAGGATCAGC
1 AGGAGGCAGTGGTGCAGCAAGAGGATCAGGAGGCGATGGTGCAGCATGAGGATCAGC
* *
138662 AGGAGG-AGGTGGTGCAGCATGAGGATCAGGAGGCGGTGGTGCAGCATGAGGATCAGC
1 AGGAGGCA-GTGGTGCAGCAAGAGGATCAGGAGGCGATGGTGCAGCATGAGGATCAGC
* * * *
138719 AGGAGGCAGTGGTGCAGCAAGAGGATCAGGAGGTGGTGGTGGTGCAGCAAGAGGATCAGG
1 AGGAGGCAGTGGTGCAGCAAGAGGATCAGGA---GGCGATGGTGCAGCATGAGGATCAGC
* ** ** *
138779 AGGTGGTGGTGGTGCCA-CGTGAGGATCAGGAGGGAACGGTGGTGCAGCATGAGGATC
1 AGGAGGCAGTGGTG-CAGCAAGAGGATCAGGA-GG--CGATGGTGCAGCATGAGGATC
138836 GGGAGAAGGT
Statistics
Matches: 149, Mismatches: 17, Indels: 13
0.83 0.09 0.07
Matches are distributed among these distances:
56 1 0.01
57 78 0.52
58 3 0.02
60 65 0.44
61 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.46, T:0.14
Consensus pattern (57 bp):
AGGAGGCAGTGGTGCAGCAAGAGGATCAGGAGGCGATGGTGCAGCATGAGGATCAGC
Found at i:138757 original size:27 final size:27
Alignment explanation
Indices: 138605--138854 Score: 212
Period size: 30 Copynumber: 8.7 Consensus size: 27
138595 GAGGAATAGG
* * * * *
138605 AGGAGGCAGTTGTGCAGCACGAGAAAC
1 AGGAGGCGGTGGTGCAGCATGAGGATC
*
138632 AGGAGGCGATGGTGCAGCATGAGGATCAGC
1 AGGAGGCGGTGGTGCAGCATGAGGAT---C
*
138662 AGGAGGAGGTGGTGCAGCATGAGGATC
1 AGGAGGCGGTGGTGCAGCATGAGGATC
138689 AGGAGGCGGTGGTGCAGCATGAGGATCAGC
1 AGGAGGCGGTGGTGCAGCATGAGGAT---C
* *
138719 AGGAGGCAGTGGTGCAGCAAGAGGATC
1 AGGAGGCGGTGGTGCAGCATGAGGATC
* *
138746 AGGAGGTGGTGGTGGTGCAGCAAGAGGATC
1 AGGA---GGCGGTGGTGCAGCATGAGGATC
* **
138776 AGGAGGTGGTGGTGGTGCCACGTGAGGATC
1 AGGAGGCGGTGGTGCAG-CA--TGAGGATC
138806 AGGAGGGAACGGTGGTGCAGCATGAGGATC
1 AGGA-GG--CGGTGGTGCAGCATGAGGATC
* **
138836 GGGAGAAGGTGGTGCAGCA
1 AGGAGGCGGTGGTGCAGCA
138855 CGAGACTCAG
Statistics
Matches: 186, Mismatches: 22, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
27 74 0.40
28 2 0.01
29 1 0.01
30 97 0.52
31 2 0.01
32 2 0.01
33 8 0.04
ACGTcount: A:0.26, C:0.14, G:0.46, T:0.14
Consensus pattern (27 bp):
AGGAGGCGGTGGTGCAGCATGAGGATC
Found at i:138791 original size:60 final size:59
Alignment explanation
Indices: 138636--138849 Score: 254
Period size: 60 Copynumber: 3.6 Consensus size: 59
138626 AGAAACAGGA
* *
138636 GGCGATGGTGCAGCATGAGGATCAGCAGGAGGAGGTGGTGCAGCATGAGGATCAGGA--
1 GGCGGTGGTGCAGCATGAGGATCAGCAGGAGGTGGTGGTGCAGCATGAGGATCAGGAGG
** *
138693 GGCGGTGGTGCAGCATGAGGATCAGCAGGAGGCAGTGGTGCAGCAAGAGGATCAGGAGG
1 GGCGGTGGTGCAGCATGAGGATCAGCAGGAGGTGGTGGTGCAGCATGAGGATCAGGAGG
* * * * *
138752 TGGTGGTGGTGCAGCAAGAGGATCAGGAGGTGGTGGTGGTGCCA-CGTGAGGATCAGGAGG
1 -GGCGGTGGTGCAGCATGAGGATCAGCAGGAGGTGGTGGTG-CAGCATGAGGATCAGGAGG
* * * *
138812 GAACGGTGGTGCAGCATGAGGATCGGGAGAAGGTGGTG
1 G-GCGGTGGTGCAGCATGAGGATCAGCAGGAGGTGGTG
138850 CAGCACGAGA
Statistics
Matches: 134, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
57 53 0.40
59 1 0.01
60 78 0.58
61 2 0.01
ACGTcount: A:0.24, C:0.13, G:0.48, T:0.15
Consensus pattern (59 bp):
GGCGGTGGTGCAGCATGAGGATCAGCAGGAGGTGGTGGTGCAGCATGAGGATCAGGAGG
Found at i:140816 original size:30 final size:30
Alignment explanation
Indices: 140782--140868 Score: 138
Period size: 30 Copynumber: 2.9 Consensus size: 30
140772 GGACCACCAT
* *
140782 CAGCTTTCGGAGGAGGTGGCGGAGGAGCAC
1 CAGCTTTTGGAGGAGGTGGAGGAGGAGCAC
140812 CAGCTTTTGGAGGAGGTGGAGGAGGAGCAC
1 CAGCTTTTGGAGGAGGTGGAGGAGGAGCAC
* *
140842 CAGCTTTTGGAGGAGGAGGAGGTGGAG
1 CAGCTTTTGGAGGAGGTGGAGGAGGAG
140869 GACCTGGTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.22, C:0.14, G:0.48, T:0.16
Consensus pattern (30 bp):
CAGCTTTTGGAGGAGGTGGAGGAGGAGCAC
Found at i:146604 original size:43 final size:43
Alignment explanation
Indices: 146557--146874 Score: 105
Period size: 40 Copynumber: 7.1 Consensus size: 43
146547 ATGAGGATGG
146557 CTGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAAT
1 CTGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAAT
* * * * * **
146600 CTGG---TCGAGGGATGACACTGCTCATACGTGATGA-AGAGTT
1 CTGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGA-AAAT
** * * * * ***
146640 CATGGCCATCTTTAGGAATGGTGATAACTCAGTTCCTACGCGATGAGGATGG
1 C-TGGTTATC--TAGG---GGTG---ACACGGTTCCTACGTGATGAGAAAAT
146692 CTGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAAT
1 CTGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAAT
* * * * * * **
146735 CTGG---TCGAGGGATGACACTGCTCATACATGATGA-AGAGTT
1 CTGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGA-AAAT
** * * ***
146775 CCTGGCCATCTTTAGAAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGT
1 -CTGGTTATC--TAG---GGGTG---ACACGGTTCCTACGTGATGA-GAAAAT
146828 -TGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAAT
1 CTGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAAT
146870 CTGGT
1 CTGGT
146875 CGAGGGATGA
Statistics
Matches: 193, Mismatches: 52, Indels: 60
0.63 0.17 0.20
Matches are distributed among these distances:
39 2 0.01
40 54 0.28
41 7 0.04
42 3 0.02
43 49 0.25
44 4 0.02
46 14 0.07
49 14 0.07
51 12 0.06
52 31 0.16
53 2 0.01
54 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
CTGGTTATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAAT
Found at i:146653 original size:135 final size:135
Alignment explanation
Indices: 146428--147133 Score: 1243
Period size: 135 Copynumber: 5.2 Consensus size: 135
146418 AGTTCGGGTC
* *
146428 ATCTAAGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
* **
146493 TGATGAAGAGTTCCTAGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTATACGATGAGGATGGC
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
146558 TGGTT
131 TGGTT
146563 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
* * *
146628 TGATGAAGAGTTCATGGCCATCTTTAGGAATGGTGATAACTCAGTTCCTACGCGATGAGGATGGC
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
146693 TGGTT
131 TGGTT
*
146698 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACA
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
* *
146763 TGATGAAGAGTTCCTGGCCATCTTTAGAAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGT
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
146828 TGGTT
131 TGGTT
146833 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
* *
146898 TGATGAAGAGTTCCTGTCCATCTTTAGGAAAGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
*
146963 TGTTT
131 TGGTT
* *
146968 ATCTAGGGGTGACATGGTTCTTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
*
147033 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGA
66 TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
147098 TGGTT
131 TGGTT
*
147103 ATCTAGGGGTGACACGGCT-CTACGTGATGAG
1 ATCTAGGGGTGACACGGTTCCTACGTGATGAG
147134 GATGACTGGC
Statistics
Matches: 542, Mismatches: 29, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
134 11 0.02
135 531 0.98
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (135 bp):
ATCTAGGGGTGACACGGTTCCTACGTGATGAGAAAATCTGGTCGAGGGATGACACTGCTCATACG
TGATGAAGAGTTCCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGATGGC
TGGTT
Found at i:147295 original size:34 final size:34
Alignment explanation
Indices: 147226--147320 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 34
147216 GACAAAATTC
* * **
147226 GTTTCAAGGGAAATGATCTCAAAGATATTTGTTTT
1 GTTTCAAGGGAAA-CAACTCAAAGATATTAATTTT
147261 GTTTCAAGGGAAACAACTCAAAGATGA-TAATTTT
1 GTTTCAAGGGAAACAACTCAAAGAT-ATTAATTTT
*
147295 GTTTCCAA-AGAAACAGACTCAAAGAT
1 GTTT-CAAGGGAAACA-ACTCAAAGAT
147321 TTTTCTTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
34 25 0.48
35 27 0.52
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (34 bp):
GTTTCAAGGGAAACAACTCAAAGATATTAATTTT
Found at i:147537 original size:27 final size:26
Alignment explanation
Indices: 147507--147576 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
147497 CTCAAAGATT
147507 ATTTTGTTAAGAGAAACAAACTCAAAG
1 ATTTT-TTAAGAGAAACAAACTCAAAG
* * * *
147534 ATTTTTCAAAAGGAACATACTCAAAG
1 ATTTTTTAAGAGAAACAAACTCAAAG
147560 ATTTATTTCAAGAGAAA
1 ATTT-TTT-AAGAGAAA
147577 TTGTCTCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 21 0.62
27 7 0.21
28 6 0.18
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.29
Consensus pattern (26 bp):
ATTTTTTAAGAGAAACAAACTCAAAG
Found at i:147651 original size:66 final size:67
Alignment explanation
Indices: 147537--147780 Score: 207
Period size: 66 Copynumber: 3.6 Consensus size: 67
147527 CTCAAAGATT
* * * * * *
147537 TTTCAAAAGGAACATACTCAAAGA-TTTATT-TCAAGAGAAATTGTCTCAATAGAGACAAAA-TT
1 TTTCCAAAGAAACAGACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAATTT
147599 CG
66 CG
* * *
147601 TTT-TAAGAGAAACAGATTCAAAGATTTTTTTCTCAAAAGAGATTGTCTCAAGAGAGACAAAATT
1 TTTCCAA-AGAAACAGACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAATT
*
147665 TTG
65 TCG
*** * *
147668 TTTCCAAAGAAACAGACTCAAAGA-TTTTTT-TCAAAAGAAA-CAACTCAA-AGATTTTTTCACG
1 TTTCCAAAGAAACAGACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGA------GACA
147729 AAATTATCTG
60 AAATT-TC-G
*
147739 TTTCAAAAGAAACAGACTCAAAGATTTTTTTCTCAAAAGAAA
1 TTTCCAAAGAAACAGACTCAAAGATTTTTTTCTCAAAAGAAA
147781 CAACTCAAAG
Statistics
Matches: 146, Mismatches: 19, Indels: 21
0.78 0.10 0.11
Matches are distributed among these distances:
63 5 0.03
64 22 0.15
65 14 0.10
66 33 0.23
67 22 0.15
68 2 0.01
69 7 0.05
70 1 0.01
71 24 0.16
72 6 0.04
73 10 0.07
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (67 bp):
TTTCCAAAGAAACAGACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAATTT
CG
Found at i:147713 original size:27 final size:28
Alignment explanation
Indices: 147658--147724 Score: 102
Period size: 28 Copynumber: 2.4 Consensus size: 28
147648 TCAAGAGAGA
*
147658 CAAA-ATTTTGTTTCCAAAGAAACAGACT
1 CAAAGATTTT-TTTCAAAAGAAACAGACT
147686 CAAAGATTTTTTTCAAAAGAAACA-ACT
1 CAAAGATTTTTTTCAAAAGAAACAGACT
147713 CAAAGATTTTTT
1 CAAAGATTTTTT
147725 CACGAAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
27 15 0.41
28 17 0.46
29 5 0.14
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAGACT
Found at i:147796 original size:28 final size:29
Alignment explanation
Indices: 147740--147823 Score: 127
Period size: 29 Copynumber: 2.9 Consensus size: 29
147730 AATTATCTGT
*
147740 TTCAAAAGAAACAGACTCAAAGATTTTTT
1 TTCAAAAGAAACAGACTCAAAGATTTTTA
147769 TCTCAAAAGAAACA-ACTCAAAGATTTTTA
1 T-TCAAAAGAAACAGACTCAAAGATTTTTA
147798 TTCAAAAG-AACAGACTCAATAGATTT
1 TTCAAAAGAAACAGACTCAA-AGATTT
147824 GTTTAAAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
27 4 0.08
28 13 0.25
29 22 0.43
30 12 0.24
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (29 bp):
TTCAAAAGAAACAGACTCAAAGATTTTTA
Found at i:147833 original size:29 final size:28
Alignment explanation
Indices: 147739--147835 Score: 121
Period size: 28 Copynumber: 3.5 Consensus size: 28
147729 AAATTATCTG
147739 TTTCAAAAGAAACAGACTCAAAGATTTTT
1 TTTCAAAAGAAACAGACTCAAAGA-TTTT
147768 TTCTCAAAAGAAACA-ACTCAAAGATTTT
1 TT-TCAAAAGAAACAGACTCAAAGATTTT
*
147796 TATTCAAAAG-AACAGACTCAATAGATTTG
1 T-TTCAAAAGAAACAGACTCAA-AGATTTT
147825 TTT-AAAA-AAAC
1 TTTCAAAAGAAAC
147836 TGTCTCAAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 12
0.83 0.01 0.16
Matches are distributed among these distances:
27 11 0.18
28 20 0.32
29 19 0.31
30 12 0.19
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.29
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:148686 original size:16 final size:16
Alignment explanation
Indices: 148665--148701 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
148655 ACTCATGTAA
*
148665 TATGTATGTGTTGATG
1 TATGTATGTATTGATG
148681 TATGTATGTATTGATG
1 TATGTATGTATTGATG
148697 TATGT
1 TATGT
148702 TTTTCTCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (16 bp):
TATGTATGTATTGATG
Done.