Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004626.1 Hibiscus syriacus cultivar Beakdansim tig00010351_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: 142111
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2829 original size:42 final size:44
Alignment explanation
Indices: 2766--2852 Score: 128
Period size: 43 Copynumber: 2.0 Consensus size: 44
2756 ACTTTAATTT
2766 TATTTCTAATTTTCTACTTGTTTTTTCATAT-AA-GATA-AACTAA
1 TATTTCTAATTTTCTACTTG--TTTTCATATAAATGATAGAACTAA
2809 TATTTCTAA-TTTCTACTTGTTTTCATATAAATGATAGAACTAA
1 TATTTCTAATTTTCTACTTGTTTTCATATAAATGATAGAACTAA
2852 T
1 T
2853 GCATATTGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
40 9 0.22
41 2 0.05
42 14 0.34
43 16 0.39
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.49
Consensus pattern (44 bp):
TATTTCTAATTTTCTACTTGTTTTCATATAAATGATAGAACTAA
Found at i:10855 original size:15 final size:16
Alignment explanation
Indices: 10824--10854 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10814 AACTTTGACC
10824 AAAAAGTCAAAATTTT
1 AAAAAGTCAAAATTTT
*
10840 AAAAAGTCATAATTT
1 AAAAAGTCAAAATTT
10855 ATGTTTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (16 bp):
AAAAAGTCAAAATTTT
Found at i:20660 original size:23 final size:23
Alignment explanation
Indices: 20630--20677 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
20620 CGCCATTTTT
20630 TACTTCTAGTGGTATTGAGTGCA
1 TACTTCTAGTGGTATTGAGTGCA
20653 TACTTCTAGTGGTATTGAGTGCA
1 TACTTCTAGTGGTATTGAGTGCA
20676 TA
1 TA
20678 TTTGTGGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (23 bp):
TACTTCTAGTGGTATTGAGTGCA
Found at i:30901 original size:15 final size:16
Alignment explanation
Indices: 30883--30912 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30873 TAACTTTTCT
30883 TTTTC-AAGTTTTTAC
1 TTTTCAAAGTTTTTAC
30898 TTTTCAAAGTTTTTA
1 TTTTCAAAGTTTTTA
30913 TTTATTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (16 bp):
TTTTCAAAGTTTTTAC
Found at i:35815 original size:18 final size:18
Alignment explanation
Indices: 35789--35823 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35779 TACGATAGGG
35789 TATGCCTTTACTCTTGGA
1 TATGCCTTTACTCTTGGA
*
35807 TATGTCTTTACTCTTGG
1 TATGCCTTTACTCTTGG
35824 TGGAGGGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.17, T:0.49
Consensus pattern (18 bp):
TATGCCTTTACTCTTGGA
Found at i:37602 original size:13 final size:13
Alignment explanation
Indices: 37584--37608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
37574 GTTTAAATAT
37584 TTTAAGAATTATC
1 TTTAAGAATTATC
37597 TTTAAGAATTAT
1 TTTAAGAATTAT
37609 ATCTTATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAAGAATTATC
Found at i:37620 original size:20 final size:20
Alignment explanation
Indices: 37592--37630 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
37582 ATTTTAAGAA
37592 TTATCTTTAAGAATTATATC
1 TTATCTTTAAGAATTATATC
* *
37612 TTATTTTTAGGAATTATAT
1 TTATCTTTAAGAATTATAT
37631 TTTCCTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (20 bp):
TTATCTTTAAGAATTATATC
Found at i:45120 original size:18 final size:18
Alignment explanation
Indices: 45094--45136 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
45084 TTTAAATTTA
* *
45094 TTTAATTAATTATTCTCT
1 TTTATTTAATTATTATCT
*
45112 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
45130 TTTATTT
1 TTTATTT
45137 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:57184 original size:24 final size:24
Alignment explanation
Indices: 57153--57200 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
57143 GAAACTGTCG
*
57153 CGTAGAATTTGCACCGAAGTGCCA
1 CGTAGAATATGCACCGAAGTGCCA
*
57177 CGTAGAATATGCACTGAAGTGCCA
1 CGTAGAATATGCACCGAAGTGCCA
57201 TATAGATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (24 bp):
CGTAGAATATGCACCGAAGTGCCA
Found at i:57206 original size:24 final size:24
Alignment explanation
Indices: 57155--57206 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
57145 AACTGTCGCG
* *
57155 TAGAATTTGCACCGAAGTGCCACG
1 TAGAATATGCACCGAAGTGCCACA
* *
57179 TAGAATATGCACTGAAGTGCCATA
1 TAGAATATGCACCGAAGTGCCACA
57203 TAGA
1 TAGA
57207 TTTATCCCGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (24 bp):
TAGAATATGCACCGAAGTGCCACA
Found at i:57229 original size:23 final size:23
Alignment explanation
Indices: 57211--57276 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
57201 TATAGATTTA
57211 TCCCGAAGGACCGCGTAGAATTG
1 TCCCGAAGGACCGCGTAGAATTG
* * *
57234 TCCCGAATGACCACATAGAATTG
1 TCCCGAAGGACCGCGTAGAATTG
*
57257 TCCCAAAGGACCGCGTAGAA
1 TCCCGAAGGACCGCGTAGAA
57277 CATTCGACTC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (23 bp):
TCCCGAAGGACCGCGTAGAATTG
Found at i:62197 original size:23 final size:23
Alignment explanation
Indices: 62163--62215 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
62153 TTTTAATAAA
62163 AAAAT-TAGTTATTAAAATGTTT
1 AAAATATAGTTATTAAAATGTTT
* * *
62185 AAAATATATTTATTAATATTTTT
1 AAAATATAGTTATTAAAATGTTT
62208 AATAATAT
1 AA-AATAT
62216 GATATATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 5 0.19
23 16 0.62
24 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AAAATATAGTTATTAAAATGTTT
Found at i:71944 original size:17 final size:17
Alignment explanation
Indices: 71918--71998 Score: 76
Period size: 17 Copynumber: 4.8 Consensus size: 17
71908 CAGTTTTTAG
71918 ATATTTACAGATATCAA
1 ATATTTACAGATATCAA
* *
71935 ATGA-TTACAGTTATCAG
1 AT-ATTTACAGATATCAA
* *
71952 ATATTTACATATATCAG
1 ATATTTACAGATATCAA
* *
71969 ATGA-TTAAAGTTATCAA
1 AT-ATTTACAGATATCAA
71986 ATATTTACAGATA
1 ATATTTACAGATA
71999 CCAGATGTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
16 2 0.04
17 46 0.92
18 2 0.04
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (17 bp):
ATATTTACAGATATCAA
Found at i:71954 original size:34 final size:34
Alignment explanation
Indices: 71916--72019 Score: 145
Period size: 34 Copynumber: 3.0 Consensus size: 34
71906 TTCAGTTTTT
*
71916 AGATATTTACAGATATCAAATGATTACAGTTATC
1 AGATATTTACAGATATCAGATGATTACAGTTATC
* *
71950 AGATATTTACATATATCAGATGATTAAAGTTATC
1 AGATATTTACAGATATCAGATGATTACAGTTATC
* * *
71984 AAATATTTACAGATACCAGATGTTTTACAGTTATC
1 AGATATTTACAGATATCAGATG-ATTACAGTTATC
72019 A
1 A
72020 TATACAAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
34 50 0.82
35 11 0.18
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (34 bp):
AGATATTTACAGATATCAGATGATTACAGTTATC
Found at i:85793 original size:34 final size:34
Alignment explanation
Indices: 85755--85861 Score: 124
Period size: 34 Copynumber: 3.1 Consensus size: 34
85745 CAGTTTTTAG
85755 ATATTTACAGATATCAAATTATTACAGTTATCAT
1 ATATTTACAGATATCAAATTATTACAGTTATCAT
* * * *
85789 ATATTTATAGATATCAGATGATTACAATTATCAT
1 ATATTTACAGATATCAAATTATTACAGTTATCAT
* * * * *
85823 ATATTTACATATACCATATGTTTTACAGTTATCAA
1 ATATTTACAGATATCAAAT-TATTACAGTTATCAT
85858 ATAT
1 ATAT
85862 AGATTAATAA
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
34 45 0.75
35 15 0.25
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (34 bp):
ATATTTACAGATATCAAATTATTACAGTTATCAT
Found at i:85830 original size:17 final size:17
Alignment explanation
Indices: 85755--85861 Score: 76
Period size: 17 Copynumber: 6.2 Consensus size: 17
85745 CAGTTTTTAG
*
85755 ATATTTACAGATATCAA
1 ATATTTACAGATATCAT
*
85772 AT-TATTACAGTTATCAT
1 ATAT-TTACAGATATCAT
* *
85789 ATATTTATAGATATCAG
1 ATATTTACAGATATCAT
85806 ATGA-TTACA-ATTATCAT
1 AT-ATTTACAGA-TATCAT
* *
85823 ATATTTACATATACCAT
1 ATATTTACAGATATCAT
* * *
85840 ATGTTTTACAGTTATCAA
1 AT-ATTTACAGATATCAT
85858 ATAT
1 ATAT
85862 AGATTAATAA
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
16 3 0.04
17 51 0.74
18 15 0.22
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (17 bp):
ATATTTACAGATATCAT
Found at i:91973 original size:20 final size:19
Alignment explanation
Indices: 91948--91988 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
91938 ACATCAGTCA
91948 GTGGGTATCGATACCAACAG
1 GTGGGTATCGATACCAA-AG
91968 GTGGGTATCGATACCAAAG
1 GTGGGTATCGATACCAAAG
91987 GT
1 GT
91989 TCAGTATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.29, C:0.17, G:0.32, T:0.22
Consensus pattern (19 bp):
GTGGGTATCGATACCAAAG
Found at i:91995 original size:20 final size:20
Alignment explanation
Indices: 91952--92001 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
91942 CAGTCAGTGG
**
91952 GTATCGATACCAACAGGTGG
1 GTATCGATACCAACAGGTCA
91972 GTATCGATACCAA-AGGTTCA
1 GTATCGATACCAACAGG-TCA
91992 GTATCGATAC
1 GTATCGATAC
92002 TTAAAGGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (20 bp):
GTATCGATACCAACAGGTCA
Found at i:95442 original size:33 final size:32
Alignment explanation
Indices: 95404--95496 Score: 88
Period size: 28 Copynumber: 3.0 Consensus size: 32
95394 CCTATTGTAA
*
95404 TTTTTTAAAAATTACTATTTTGGTC-CCTAAACT
1 TTTTTTAAAAATTA-TACTTTGGTCACC-AAACT
**
95437 TTTTTTAAAGTTTATACTTTGGTCACCAAAC-
1 TTTTTTAAAAATTATACTTTGGTCACCAAACT
* *
95468 ---TTTAAAAATTATAATTTGGTCACTAAACT
1 TTTTTTAAAAATTATACTTTGGTCACCAAACT
95497 AAATCCATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
28 24 0.47
32 13 0.25
33 14 0.27
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (32 bp):
TTTTTTAAAAATTATACTTTGGTCACCAAACT
Found at i:100544 original size:30 final size:30
Alignment explanation
Indices: 100484--100544 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
100474 CTCAAACTAT
* **
100484 TATTATTTTATTATATATATAATATTAATA
1 TATTATTTTAGTATATATATAATAAAAATA
*
100514 TATTATTTTAGTATCAT-TTTAATAAAAATA
1 TATTATTTTAGTAT-ATATATAATAAAAATA
100544 T
1 T
100545 TAATTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
TATTATTTTAGTATATATATAATAAAAATA
Found at i:100595 original size:21 final size:21
Alignment explanation
Indices: 100571--100614 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
100561 TTTATTGATG
100571 ATTTTAATAAT-ATAATATAAT
1 ATTTTAATAATAAT-ATATAAT
* *
100592 ATTTTTATTATAATATATAAT
1 ATTTTAATAATAATATATAAT
100613 AT
1 AT
100615 CATACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTTAATAATAATATATAAT
Found at i:100704 original size:27 final size:26
Alignment explanation
Indices: 100629--100704 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 26
100619 CTTTTGTTTT
*
100629 ATTAATATATAATAAATTATTTATAAAA
1 ATTAATAT-T-ATTAATTATTTATAAAA
*
100657 ATTAATATTATTTATTAATTTCATAAAA
1 ATTAATATTATTAATT-ATTT-ATAAAA
100685 A-TAATATTATTGAATTATTT
1 ATTAATATTATT-AATTATTT
100705 TTTATTAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 5 0.12
27 19 0.45
28 18 0.43
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (26 bp):
ATTAATATTATTAATTATTTATAAAA
Found at i:100936 original size:24 final size:26
Alignment explanation
Indices: 100909--100956 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
100899 TAATATTCCC
100909 ATTTAAATAA-AATATT-TTTTAAAT
1 ATTTAAATAATAATATTATTTTAAAT
* *
100933 ATTTTAATAATATTATTATTTTAA
1 ATTTAAATAATAATATTATTTTAA
100957 TAAGTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 5 0.25
26 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTAAATAATAATATTATTTTAAAT
Found at i:100954 original size:17 final size:17
Alignment explanation
Indices: 100932--100988 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
100922 ATTTTTTAAA
100932 TATTTTAATAATATTAT
1 TATTTTAATAATATTAT
*
100949 TATTTTAATAAGTAATTAA
1 TATTTTAATAA-T-ATTAT
*
100968 TATAATTAATAATA-TAT
1 TAT-TTTAATAATATTAT
100985 TATT
1 TATT
100989 CTTATTTTAC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 16 0.48
18 2 0.06
19 8 0.24
20 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
TATTTTAATAATATTAT
Found at i:104367 original size:14 final size:14
Alignment explanation
Indices: 104348--104378 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
104338 TGAGAAGTAT
104348 AATTTATTTTATGA
1 AATTTATTTTATGA
*
104362 AATTTATTTTTTGA
1 AATTTATTTTATGA
104376 AAT
1 AAT
104379 ATGTTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (14 bp):
AATTTATTTTATGA
Found at i:108451 original size:24 final size:24
Alignment explanation
Indices: 108392--108458 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
108382 GAGATCTTTT
*
108392 TAAATTTTATTAGTTTAATTTAATATA
1 TAAA-TTTATTA-TATAA-TTAATATA
108419 TAAATTTATTA-ATAATTAA-ATA
1 TAAATTTATTATATAATTAATATA
108441 TACAATATTATTATATAA
1 TA-AAT-TTATTATATAA
108459 AAAATAAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 5 0.14
23 7 0.19
24 9 0.25
25 4 0.11
26 7 0.19
27 4 0.11
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (24 bp):
TAAATTTATTATATAATTAATATA
Found at i:108463 original size:24 final size:22
Alignment explanation
Indices: 108416--108464 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 22
108406 TTAATTTAAT
*
108416 ATATAAATTTATTAATAATTAA
1 ATATAAATTTATTAATAATAAA
108438 ATATACAATATTATTATATAA-AAA
1 ATATA-AAT-TTATTA-ATAATAAA
108462 ATA
1 ATA
108465 AATGTAATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 5 0.22
23 3 0.13
24 11 0.48
25 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATAAATTTATTAATAATAAA
Found at i:110664 original size:2 final size:2
Alignment explanation
Indices: 110657--110682 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
110647 ACTGCCATAA
110657 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
110683 TTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114492 original size:2 final size:2
Alignment explanation
Indices: 114487--114550 Score: 57
Period size: 2 Copynumber: 33.5 Consensus size: 2
114477 TTAAAACAAC
114487 TA TA TA TA TA TA TA TA TA -A CTA TA TA -A TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
114526 TA TA GTG TA TA TA TA AA T- TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA T
114551 GAATTTTATA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
1 5 0.10
2 44 0.86
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:114547 original size:11 final size:11
Alignment explanation
Indices: 114487--114699 Score: 53
Period size: 11 Copynumber: 18.7 Consensus size: 11
114477 TTAAAACAAC
*
114487 TATATATATA-
1 TATATATAAAT
*
114497 TATATAT-AAC
1 TATATATAAAT
114507 TATATAATAATAT
1 TATAT-ATAA-AT
* *
114520 AATATATATAGT
1 TATATATA-AAT
114532 GTATATATAAAT
1 -TATATATAAAT
*
114544 TATATATGAAT
1 TATATATAAAT
* *
114555 TTTATATGCAATT
1 TATATAT--AAAT
**
114568 TATATATAGTT
1 TATATATAAAT
*
114579 TATATTTATATAT
1 TATA--TATAAAT
* *
114592 TATGTAT-TAT
1 TATATATAAAT
114602 GTATAATTATAAA-
1 -TAT-A-TATAAAT
* *
114615 TA-ATATATAC
1 TATATATAAAT
*
114625 TATGTATAAAT
1 TATATATAAAT
**
114636 TATATAGTTTAT
1 TATATA-TAAAT
*
114648 TA-ATATAAAC
1 TATATATAAAT
*
114658 TATATATAAAC
1 TATATATAAAT
* *
114669 AATATATACTAAC
1 TATATATA--AAT
*
114682 T-TATATAAAC
1 TATATATAAAT
114692 TATATATA
1 TATATATA
114700 GGGATGGCAA
Statistics
Matches: 153, Mismatches: 29, Indels: 41
0.69 0.13 0.18
Matches are distributed among these distances:
9 6 0.04
10 26 0.17
11 65 0.42
12 20 0.13
13 35 0.23
14 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (11 bp):
TATATATAAAT
Found at i:114573 original size:13 final size:12
Alignment explanation
Indices: 114533--114583 Score: 54
Period size: 11 Copynumber: 4.4 Consensus size: 12
114523 ATATATAGTG
*
114533 TATATAT-AAAT
1 TATATATGAATT
114544 TATATATGAATT
1 TATATATGAATT
114556 T-TATATGCAATT
1 TATATATG-AATT
*
114568 TATATAT-AGTT
1 TATATATGAATT
114579 TATAT
1 TATAT
114584 TTATATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 21 0.60
12 9 0.26
13 5 0.14
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (12 bp):
TATATATGAATT
Found at i:114690 original size:23 final size:24
Alignment explanation
Indices: 114655--114699 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
114645 TATTAATATA
114655 AACTATATATAAACAATATATACT
1 AACTATATATAAACAATATATACT
*
114679 AACT-TATATAAACTATATATA
1 AACTATATATAAACAATATATA
114700 GGGATGGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (24 bp):
AACTATATATAAACAATATATACT
Found at i:114876 original size:15 final size:15
Alignment explanation
Indices: 114856--114890 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
114846 AGACATTACA
*
114856 CGCCCCGCATCCGCC
1 CGCCCCACATCCGCC
114871 CGCCCCACATCCGCC
1 CGCCCCACATCCGCC
114886 CGCCC
1 CGCCC
114891 AACTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.09, C:0.69, G:0.17, T:0.06
Consensus pattern (15 bp):
CGCCCCACATCCGCC
Found at i:115747 original size:15 final size:15
Alignment explanation
Indices: 115727--115760 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
115717 ACATATGAAT
115727 TATATGTATAAACTA
1 TATATGTATAAACTA
115742 TATATGTATAAACTA
1 TATATGTATAAACTA
115757 TATA
1 TATA
115761 AACTATGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (15 bp):
TATATGTATAAACTA
Found at i:115820 original size:32 final size:33
Alignment explanation
Indices: 115779--115878 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 33
115769 AAACTATATA
** *
115779 ATATATATAGTTTAGTAATTTAC-ATATGAACT
1 ATATATATAGTTTAGTAATGAACTATATAAACT
*
115811 ATATATATAGTTTATTAATGAACTATATAAACT
1 ATATATATAGTTTAGTAATGAACTATATAAACT
* *
115844 ATATATATAGTATA-TACT-ATA-TATATAAACT
1 ATATATATAGTTTAGTAATGA-ACTATATAAACT
115875 ATAT
1 ATAT
115879 TTTATATTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
31 15 0.25
32 24 0.40
33 21 0.35
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (33 bp):
ATATATATAGTTTAGTAATGAACTATATAAACT
Found at i:115877 original size:20 final size:20
Alignment explanation
Indices: 115831--115953 Score: 69
Period size: 20 Copynumber: 6.0 Consensus size: 20
115821 TTTATTAATG
115831 AACTATATAAACTATATATAT-
1 AACTATAT--ACTATATATATA
*
115852 -AGTATATACTATATATATA
1 AACTATATACTATATATATA
** *
115871 AACTATATTTTATATTTATA
1 AACTATATACTATATATATA
* *
115891 TACTACATACTATAGTTGATATTTA
1 AACTATATACTATA--T-ATA--TA
115916 TATACTATAT--TATATATATA
1 -A-ACTATATACTATATATATA
115936 AACTATATA-TA-ATATATA
1 AACTATATACTATATATATA
115954 GTATAGTTTA
Statistics
Matches: 80, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
18 25 0.31
19 3 0.04
20 33 0.41
22 4 0.05
23 3 0.04
25 6 0.08
27 6 0.08
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (20 bp):
AACTATATACTATATATATA
Found at i:115942 original size:11 final size:11
Alignment explanation
Indices: 115928--115998 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
115918 TACTATATTA
115928 TATATATAAAC
1 TATATATAAAC
115939 TATATATAATA-
1 TATATATAA-AC
***
115950 TATAGTATAGTT
1 TATA-TATAAAC
* *
115962 TACATATGAAC
1 TATATATAAAC
*
115973 TATATATAAAA
1 TATATATAAAC
*
115984 TCTATATAAAC
1 TATATATAAAC
115995 TATA
1 TATA
115999 GTTTATATAT
Statistics
Matches: 44, Mismatches: 13, Indels: 6
0.70 0.21 0.10
Matches are distributed among these distances:
11 36 0.82
12 8 0.18
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (11 bp):
TATATATAAAC
Found at i:115944 original size:74 final size:71
Alignment explanation
Indices: 115843--116074 Score: 162
Period size: 74 Copynumber: 3.3 Consensus size: 71
115833 CTATATAAAC
*
115843 TATATA-TATAGTATATACTAT--ATATATAAACTATATTTTATATTTATATACTACATACTATA
1 TATATACTATATTATATA-TATAAATATATAAACTATATTTTATATTTATATACTACATACTATA
115905 GTTGATATT
65 GTT-A-ATT
** *
115914 TATATACTATATTATATATATAAACTATATATAA-TATATAGTATAGTTTACATA-TGA-ACTA-
1 TATATACTATATTATATATATAAA-TATATA-AACTATATTTTATA-TTTATATACT-ACA-TAC
*
115975 TATA-TAAAATCT
61 TATAGT-TAAT-T
* * * * **
115987 ATATAAACTATAGTT-TATATATAAAT-TATATACTATAGTTGATATTTATATACTATGTACTAT
1 -TATATACTATA-TTATATATATAAATATATAAACTATATTTTATATTTATATACTACATACTAT
*
116050 AGTTAATA
64 AGTTAATT
*
116058 T-TATACTATATAATATA
1 TATATACTATATTATATA
116075 AAAATTCAAA
Statistics
Matches: 126, Mismatches: 17, Indels: 38
0.70 0.09 0.21
Matches are distributed among these distances:
68 1 0.01
69 12 0.10
70 1 0.01
71 20 0.16
72 31 0.25
73 6 0.05
74 41 0.33
75 14 0.11
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (71 bp):
TATATACTATATTATATATATAAATATATAAACTATATTTTATATTTATATACTACATACTATAG
TTAATT
Found at i:115952 original size:34 final size:34
Alignment explanation
Indices: 115914--116018 Score: 95
Period size: 34 Copynumber: 2.9 Consensus size: 34
115904 AGTTGATATT
*
115914 TATATACTATA-TTATATATATAAACTATATATAA
1 TATATACTATAGTT-TACATATAAACTATATATAA
* *
115948 TATATAGTATAGTTTACATATGAACTATATATAAAA
1 TATATACTATAGTTTACATATAAACTATATAT--AA
* *
115984 TCTATATAAACTATAGTTTATATATAAATTATATA
1 --TATAT--ACTATAGTTTACATATAAACTATATA
116019 CTATAGTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
34 26 0.46
35 2 0.04
36 2 0.04
38 5 0.09
40 22 0.39
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.43
Consensus pattern (34 bp):
TATATACTATAGTTTACATATAAACTATATATAA
Found at i:116036 original size:27 final size:26
Alignment explanation
Indices: 115988--116074 Score: 74
Period size: 27 Copynumber: 3.4 Consensus size: 26
115978 ATAAAATCTA
* * *
115988 TATAAACTATAGTT-TATATATAAAT
1 TATATACTATAGTTATATTTATAAAC
*
116013 TATATACTATAGTTGATATTTATATAC
1 TATATACTATAGTT-ATATTTATAAAC
*
116040 TATGTACTATAGTTA-ATATTAT--AC
1 TATATACTATAGTTATAT-TTATAAAC
*
116064 TATATAATATA
1 TATATACTATA
116075 AAAATTCAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
24 11 0.21
25 15 0.29
26 5 0.10
27 21 0.40
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (26 bp):
TATATACTATAGTTATATTTATAAAC
Found at i:118083 original size:6 final size:6
Alignment explanation
Indices: 118072--118098 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
118062 ACCATTGTCG
118072 CATCTC CATCTC CATCTC CATCTC CAT
1 CATCTC CATCTC CATCTC CATCTC CAT
118099 GTTCTCCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.48, G:0.00, T:0.33
Consensus pattern (6 bp):
CATCTC
Found at i:123202 original size:82 final size:82
Alignment explanation
Indices: 123102--123375 Score: 225
Period size: 82 Copynumber: 3.3 Consensus size: 82
123092 TTAGACAAAC
* * *
123102 GCCGCGATATCCTA-ATATATAGTGGTATTTTTGGGAAAATGCCACTACAAACTCATAATTTAGT
1 GCCGCGATAGCC-AGATATATAGTGGTATTTTTGGGAAAATGCCGCTACAAACTCATACTTTAGT
*
123166 GGCATTTATATAAAAAAA
65 GGCATTTATGTAAAAAAA
* * * * **
123184 GCCGCGATAGCCAGATATATAGTGG-CTTTTTGTG-AAATCACCGCTA-AAAATGGTTACTTTAG
1 GCCGCGATAGCCAGATATATAGTGGTATTTTTGGGAAAAT-GCCGCTACAAACT-CATACTTTAG
123246 TGGCATTTATGTAAACAAAA
64 TGGCATTTATGTAAA-AAAA
** * * *** * *
123266 TGGCCGTTATAGCTAGATATATAGCGACGTTTTT-GTATAAATGCCGCTACAAACGCATACTTTA
1 --GCCGCGATAGCCAGATATATAGTGGTATTTTTGGGA-AAATGCCGCTACAAACTCATACTTTA
* *
123330 GTGGCGTTTATGTAAAAAAC
63 GTGGCATTTATGTAAAAAAA
* * * *
123350 GCTGCTATAACCCGATATATAGTGGT
1 GCCGCGATAGCCAGATATATAGTGGT
123376 GTTTGTGTAG
Statistics
Matches: 149, Mismatches: 33, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
80 8 0.05
81 34 0.23
82 44 0.30
84 23 0.15
85 33 0.22
86 7 0.05
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (82 bp):
GCCGCGATAGCCAGATATATAGTGGTATTTTTGGGAAAATGCCGCTACAAACTCATACTTTAGTG
GCATTTATGTAAAAAAA
Found at i:123327 original size:85 final size:80
Alignment explanation
Indices: 123129--123371 Score: 225
Period size: 85 Copynumber: 3.0 Consensus size: 80
123119 TATAGTGGTA
* * * * *
123129 TTTTTGGGAAAATGCCACTACAAACTCATAATTTAGTGGCATTTATATAAAAAAAGCCGCGATAG
1 TTTTTGTG-AAATGCCGCTACAAACGCATACTTTAGTGGCATTTATGTAAAAAAAGCCGCGATAG
* *
123194 CCAGATATATAGTGGC
65 CCAGATATATAGCGAC
* * * ** **
123210 TTTTTGTGAAATCACCGCTAAAAATGGTTACTTTAGTGGCATTTATGTAAACAAAATGGCCGTTA
1 TTTTTGTGAAAT-GCCGCTACAAACGCATACTTTAGTGGCATTTATGTAAA-AAAA--GCCGCGA
*
123275 TAGCTAGATATATAGCGAC
62 TAGCCAGATATATAGCGAC
* * * * *
123294 GTTTTTGTATAAATGCCGCTACAAACGCATACTTTAGTGGCGTTTATGTAAAAAACGCTGCTATA
1 -TTTTTGT-GAAATGCCGCTACAAACGCATACTTTAGTGGCATTTATGTAAAAAAAGCCGCGATA
* *
123359 ACCCGATATATAG
64 GCCAGATATATAG
123372 TGGTGTTTGT
Statistics
Matches: 128, Mismatches: 28, Indels: 11
0.77 0.17 0.07
Matches are distributed among these distances:
80 4 0.03
81 36 0.28
82 21 0.16
84 24 0.19
85 39 0.30
86 4 0.03
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (80 bp):
TTTTTGTGAAATGCCGCTACAAACGCATACTTTAGTGGCATTTATGTAAAAAAAGCCGCGATAGC
CAGATATATAGCGAC
Found at i:123649 original size:12 final size:12
Alignment explanation
Indices: 123632--123676 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
123622 ACTATACGTT
*
123632 ATGAACAATACC
1 ATGAACAGTACC
**
123644 ATGAACAGTGTC
1 ATGAACAGTACC
123656 ATGAACAGTACC
1 ATGAACAGTACC
123668 ATGAACAGT
1 ATGAACAGT
123677 GAAAAAATTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:123667 original size:24 final size:24
Alignment explanation
Indices: 123632--123677 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
123622 ACTATACGTT
123632 ATGAACAATACCATGAACAGTGTC
1 ATGAACAATACCATGAACAGTGTC
*
123656 ATGAACAGTACCATGAACAGTG
1 ATGAACAATACCATGAACAGTG
123678 AAAAAATTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (24 bp):
ATGAACAATACCATGAACAGTGTC
Found at i:127456 original size:45 final size:47
Alignment explanation
Indices: 127397--127485 Score: 137
Period size: 45 Copynumber: 1.9 Consensus size: 47
127387 TCGAATAAAT
*
127397 GCATGCGAACTAGATATCATGCGATTAGG-TTTATTTTT-TGAACAA
1 GCATACGAACTAGATATCATGCGATTAGGATTTATTTTTGTGAACAA
* *
127442 GCATACGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATACGAACTAGATATCATGCGATTAGGATTTATTTTTGTGAA
127486 TAACAAAGCA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 26 0.67
46 9 0.23
47 4 0.10
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (47 bp):
GCATACGAACTAGATATCATGCGATTAGGATTTATTTTTGTGAACAA
Found at i:137100 original size:8 final size:8
Alignment explanation
Indices: 137083--137245 Score: 72
Period size: 8 Copynumber: 20.1 Consensus size: 8
137073 CTTAAAGAAT
*
137083 AAATGGAA
1 AAATGAAA
137091 AAATGAAA
1 AAATGAAA
137099 AAATGAAAA
1 AAATG-AAA
137108 AAATGAAA
1 AAATGAAA
*
137116 AAA-AAGAA
1 AAATGA-AA
137124 AAATGAGAA
1 AAATGA-AA
137133 AAATGAGAA
1 AAATGA-AA
*
137142 AAA--AAG
1 AAATGAAA
*
137148 AAAT-AGA
1 AAATGAAA
**
137155 AAATGGGA
1 AAATGAAA
**
137163 AAATGGTA
1 AAATGAAA
**
137171 AAATGGGA
1 AAATGAAA
137179 AAATAGAAGA
1 AAAT-GAA-A
*
137189 AAA--AAG
1 AAATGAAA
137195 AAATGAAA
1 AAATGAAA
137203 AAATGACGAA
1 AAATGA--AA
137213 AAATG-AA
1 AAATGAAA
*
137220 AACTGAAA
1 AAATGAAA
137228 AAATAGAGAA
1 AAAT-GA-AA
137238 AAAT-AAA
1 AAATGAAA
137245 A
1 A
137246 GGGGTTCAAG
Statistics
Matches: 126, Mismatches: 15, Indels: 29
0.74 0.09 0.17
Matches are distributed among these distances:
6 7 0.06
7 18 0.14
8 57 0.45
9 27 0.21
10 17 0.13
ACGTcount: A:0.69, C:0.01, G:0.18, T:0.11
Consensus pattern (8 bp):
AAATGAAA
Found at i:137108 original size:9 final size:9
Alignment explanation
Indices: 137089--137150 Score: 67
Period size: 9 Copynumber: 7.1 Consensus size: 9
137079 GAATAAATGG
137089 AAAAATG-A
1 AAAAATGAA
137097 AAAAATGAA
1 AAAAATGAA
137106 AAAAATGAA
1 AAAAATGAA
*
137115 AAAAA--AG
1 AAAAATGAA
*
137122 AAAAATGAG
1 AAAAATGAA
137131 AAAAATGAGA
1 AAAAATGA-A
*
137141 AAAAAAGAA
1 AAAAATGAA
137150 A
1 A
137151 TAGAAAATGG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
7 6 0.13
8 7 0.15
9 27 0.57
10 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (9 bp):
AAAAATGAA
Found at i:137117 original size:25 final size:25
Alignment explanation
Indices: 137097--137150 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
137087 GGAAAAATGA
137097 AAAAATGAAAAAAATGAAAAAAAAG
1 AAAAATGAAAAAAATGAAAAAAAAG
*
137122 AAAAATGAGAAAAATGAGAAAAAAAG
1 AAAAATGAAAAAAATGA-AAAAAAAG
137148 AAA
1 AAA
137151 TAGAAAATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 16 0.59
26 11 0.41
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (25 bp):
AAAAATGAAAAAAATGAAAAAAAAG
Found at i:138638 original size:55 final size:55
Alignment explanation
Indices: 138595--138980 Score: 280
Period size: 55 Copynumber: 7.2 Consensus size: 55
138585 GTTGAAGATT
* *
138595 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGATAGTTC
* ** * *
138650 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCTGTT-TTATGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGT-TGAAGATAGTTC
* * ** * *
138705 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGGCCCGTT-TTTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGATAGTTC
** * * *
138759 GAGTTATATACTCTTTGAAGGAATAGAGAGC--CCCA-TT-GTTGAAG--A-TTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGATAGTTC
* * *
138807 GAGTTCTATACTCTCTGAAGGAATAG-GA--GGACACGTT--TATGAAGATTGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGT-TGAAGATAGTTC
* * * ** ** *
138858 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
1 GAGTCCTATACTCTCTGAA-GGAATAGAGAGCGGACAAGTTCGTTGAAGATAGTTC
* * * * * * * * **
138913 GAGTCTTATACTCCCTAAATGAATAGGGAGCAGACACGTTTGCCGAAGATAGTTC
1 GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGATAGTTC
*
138968 GAGTCTTATACTC
1 GAGTCCTATACTC
138981 CTTAAAAGAA
Statistics
Matches: 285, Mismatches: 31, Indels: 30
0.82 0.09 0.09
Matches are distributed among these distances:
47 4 0.01
48 34 0.12
51 33 0.12
52 6 0.02
54 51 0.18
55 156 0.55
56 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (55 bp):
GAGTCCTATACTCTCTGAAGGAATAGAGAGCGGACAAGTTCGTTGAAGATAGTTC
Found at i:139017 original size:55 final size:55
Alignment explanation
Indices: 138836--138999 Score: 170
Period size: 55 Copynumber: 3.0 Consensus size: 55
138826 GGAATAGGAG
* * * * * * *
138836 GACACGTTT-ATGAAGATTGTTCGAGT-TCTATACTCCCTGAACGGATAGGGAGCG
1 GACACGTTTGTTGAAGATAGTTCGAGTCT-TATACTCCCTAAAAGAATAGGGAACA
* * * * *
138890 GACCCGTTTATTGAAGATTGTTCGAGTCTTATACTCCCTAAATGAATAGGGAGCA
1 GACACGTTTGTTGAAGATAGTTCGAGTCTTATACTCCCTAAAAGAATAGGGAACA
** *
138945 GACACGTTTGCCGAAGATAGTTCGAGTCTTATACTCCTTAAAAGAATAGGGAACA
1 GACACGTTTGTTGAAGATAGTTCGAGTCTTATACTCCCTAAAAGAATAGGGAACA
139000 TACCTGTTAT
Statistics
Matches: 94, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
54 8 0.09
55 85 0.90
56 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (55 bp):
GACACGTTTGTTGAAGATAGTTCGAGTCTTATACTCCCTAAAAGAATAGGGAACA
Done.