Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001430.1 Hibiscus syriacus cultivar Beakdansim tig00002776_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: 76494
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2392 original size:50 final size:51
Alignment explanation
Indices: 2299--2401 Score: 154
Period size: 50 Copynumber: 2.0 Consensus size: 51
2289 AGGTTTCATG
* *
2299 TCACTCGAGATATCTTCCCTCGAAGCTCAAAAACATTTCAACAATTTTATC
1 TCACTCGAGATAACTTCCCTAGAAGCTCAAAAACATTTCAACAATTTTATC
* * *
2350 TCACTCGAGATAACTT-CCTAGGAGCTCAAAATCATTTTAACAATTTTATC
1 TCACTCGAGATAACTTCCCTAGAAGCTCAAAAACATTTCAACAATTTTATC
2400 TC
1 TC
2402 GCAAGATTAC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 32 0.68
51 15 0.32
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (51 bp):
TCACTCGAGATAACTTCCCTAGAAGCTCAAAAACATTTCAACAATTTTATC
Found at i:2457 original size:134 final size:138
Alignment explanation
Indices: 2186--2470 Score: 364
Period size: 134 Copynumber: 2.1 Consensus size: 138
2176 GAAAATCATT
* ** *
2186 TCAAAAACATTTCAAAATTTTTATCTCGCTCAAGATAGTTTCCCTAGAATCTCAAAATCATTTCA
1 TCAAAAACATTTCAAAATTTTTATCTCACTCAAGATAACTTCCCTAGAAGCTCAAAATCATTTCA
* * ** * * *
2251 ACAATTTTATCCCACTCGAGATTGTTTTTCTTAAAACAAGGTTTCATGTCACTCGAGATATCTTC
66 ACAATTTTAT-CCACGCAAGATTACTTTTCTTAAAACAAGATTTCATCTCACTCGAGATAGCTTC
2316 CCTCGAAGC
130 CCTCGAAGC
* * *
2325 TCAAAAACATTTCAACAA-TTTTATCTCACTCGAGATAACTT-CCTAGGAGCTCAAAATCATTTT
1 TCAAAAACATTTCAA-AATTTTTATCTCACTCAAGATAACTTCCCTAGAAGCTCAAAATCATTTC
*
2388 AACAATTTTAT-CTCGCAAGATTACTTTTCTT-AAA-AAGATTTCATCTCACTCGAGATAGCTTC
65 AACAATTTTATCCACGCAAGATTACTTTTCTTAAAACAAGATTTCATCTCACTCGAGATAGCTTC
2450 CCTCGAAGC
130 CCTCGAAGC
* *
2459 TTAAAATCATTT
1 TCAAAAACATTT
2471 ATTTTTCAAC
Statistics
Matches: 128, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
134 44 0.34
135 3 0.02
136 15 0.12
138 30 0.23
139 34 0.27
140 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.35
Consensus pattern (138 bp):
TCAAAAACATTTCAAAATTTTTATCTCACTCAAGATAACTTCCCTAGAAGCTCAAAATCATTTCA
ACAATTTTATCCACGCAAGATTACTTTTCTTAAAACAAGATTTCATCTCACTCGAGATAGCTTCC
CTCGAAGC
Found at i:6487 original size:63 final size:63
Alignment explanation
Indices: 6415--6537 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 63
6405 ACGAGTCGAG
* * * * *
6415 TTTAACGAGCAATGAGTCAAGTTGAGCAGCAAATTTTTTTAACAATCGCGAGTCGAGCACAAT
1 TTTAACGAGCAACGAGTCAAGTCGAGCAGCAAAATTTTTTAACAAGCACGAGTCGAGCACAAT
*
6478 TTTAACGAGCAACGAGTCAAGTCGAGCAGCAAAATTTTTTAATAAGCACGAGTCGAGCAC
1 TTTAACGAGCAACGAGTCAAGTCGAGCAGCAAAATTTTTTAACAAGCACGAGTCGAGCAC
6538 TGTCCAACTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (63 bp):
TTTAACGAGCAACGAGTCAAGTCGAGCAGCAAAATTTTTTAACAAGCACGAGTCGAGCACAAT
Found at i:12049 original size:36 final size:37
Alignment explanation
Indices: 12002--12072 Score: 135
Period size: 36 Copynumber: 1.9 Consensus size: 37
11992 AGACAACCCC
12002 TTTCTTAATATTAAAAAATAAATAAATA-TATTTAAT
1 TTTCTTAATATTAAAAAATAAATAAATATTATTTAAT
12038 TTTCTTAATATTAAAAAATAAATAAATATTATTTA
1 TTTCTTAATATTAAAAAATAAATAAATATTATTTA
12073 TGTAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 28 0.82
37 6 0.18
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (37 bp):
TTTCTTAATATTAAAAAATAAATAAATATTATTTAAT
Found at i:12085 original size:37 final size:36
Alignment explanation
Indices: 12006--12081 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
11996 AACCCCTTTC
* **
12006 TTAATATTAAAAAATAAATAAATATATTTAATTTTC
1 TTAATATTAAAAAATAAATAAATATATTTAATGTAA
12042 TTAATATTAAAAAATAAATAAATATTATTT-ATGTAA
1 TTAATATTAAAAAATAAATAAATA-TATTTAATGTAA
12078 TTAA
1 TTAA
12082 ATATATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 31 0.86
37 5 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (36 bp):
TTAATATTAAAAAATAAATAAATATATTTAATGTAA
Found at i:12104 original size:22 final size:23
Alignment explanation
Indices: 12056--12109 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
12046 TATTAAAAAA
* *
12056 TAAATAAATATTATTTATGTAAT
1 TAAATAAATATTATTTATATAAC
* *
12079 TAAATATATA-TATTTATATGAC
1 TAAATAAATATTATTTATATAAC
12101 TAAAATAAA
1 T-AAATAAA
12110 ATAAAATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAATAAATATTATTTATATAAC
Found at i:13811 original size:84 final size:82
Alignment explanation
Indices: 13651--13815 Score: 233
Period size: 84 Copynumber: 2.0 Consensus size: 82
13641 GATTAAGATG
* * *
13651 GAAATATTAATGCTGATCTATCTCCTTCTGCGATGAATCGAGCTAAGGTTGAACAAGTTCTTCAG
1 GAAATACTAATGATGATCTATCTCCTTCTGCGATGAATCGAGCAAAGGTTGAACAAGTTCTTCAG
*
13716 ATATTGAACTTCTTCTA
66 ATATTAAACTTCTTCTA
* * *
13733 GAAATACTAATGATGCTCTATTTCCTTCTGCGATAGAATCGAGCAAAAGGTTGAATAAGTTCTTC
1 GAAATACTAATGATGATCTATCTCCTTCTGCGAT-GAATCGAGC-AAAGGTTGAACAAGTTCTTC
13798 AGAT-TATAAACTTCTTCT
64 AGATAT-TAAACTTCTTCT
13816 TCCTCTTATG
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 30 0.41
83 10 0.14
84 33 0.45
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (82 bp):
GAAATACTAATGATGATCTATCTCCTTCTGCGATGAATCGAGCAAAGGTTGAACAAGTTCTTCAG
ATATTAAACTTCTTCTA
Found at i:13925 original size:123 final size:123
Alignment explanation
Indices: 13721--14111 Score: 559
Period size: 123 Copynumber: 3.2 Consensus size: 123
13711 TTCAGATATT
* ** * * * * *
13721 GAACTTCTTCTAGAAATACTAATGATGCTCTATTTCCTTCTGCGATAGAATCGAGCAAAAGGTTG
1 GAACTCCTTCTAGAAATGTTGATGCTACTCTATCTCCTTCTGCAATAGAATCGAGCAAAAGGTTG
* *
13786 AATAAGTTCTTCAGATTATAAACTTCTTCTTCCTCTT-ATGATGAGTTCTTCTTATTAT
66 AATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCA-GATGAGTTCTTCTTATTAC
* * * *
13844 GAACTCCTTCTGGAAATGTTGATGCTACTCTATCTCCTTCTGTAATAGAATCAAGCAAAATGTTG
1 GAACTCCTTCTAGAAATGTTGATGCTACTCTATCTCCTTCTGCAATAGAATCGAGCAAAAGGTTG
* *
13909 AATAAGTTCTTTAGATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
66 AATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
* * * * * *
13967 GAACTCCTTTTAGAAATGTTAATGTTGCTCTATCTCCTTTTGCAATAGAGTCGAGCAAAAGGTTG
1 GAACTCCTTCTAGAAATGTTGATGCTACTCTATCTCCTTCTGCAATAGAATCGAGCAAAAGGTTG
*
14032 AATAAGTTCTTCATATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
66 AATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
14090 GAACTCCTTCTAGAAATGTTGA
1 GAACTCCTTCTAGAAATGTTGA
14112 AAACATTCTG
Statistics
Matches: 236, Mismatches: 31, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
123 235 1.00
124 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (123 bp):
GAACTCCTTCTAGAAATGTTGATGCTACTCTATCTCCTTCTGCAATAGAATCGAGCAAAAGGTTG
AATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
Found at i:16890 original size:18 final size:19
Alignment explanation
Indices: 16851--16892 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
16841 TGTCATTTTC
*
16851 TTTTATTTTTTTTATCTTTA
1 TTTTATTTTTTATATC-TTA
16871 TTTTATTTTTTATATC-TA
1 TTTTATTTTTTATATCTTA
16889 TTTT
1 TTTT
16893 GTTTAGGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTATTTTTTATATCTTA
Found at i:19131 original size:12 final size:12
Alignment explanation
Indices: 19114--19138 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19104 AATATATATT
19114 TTCTTGTAATTA
1 TTCTTGTAATTA
19126 TTCTTGTAATTA
1 TTCTTGTAATTA
19138 T
1 T
19139 AAAATACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTCTTGTAATTA
Found at i:20561 original size:25 final size:28
Alignment explanation
Indices: 20533--20595 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 28
20523 GCTCTGTTTA
*
20533 TTTTAGAAAATA-TTTTTA-TTT-AATT
1 TTTTAGAAAATAGTTTTCATTTTCAATT
*
20558 TTTTAGAAATTAGTTTTCATTTTCAATT
1 TTTTAGAAAATAGTTTTCATTTTCAATT
20586 TTTTA-AAAAT
1 TTTTAGAAAAT
20596 TAAAAAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.34
26 5 0.16
27 7 0.22
28 9 0.28
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (28 bp):
TTTTAGAAAATAGTTTTCATTTTCAATT
Found at i:21014 original size:30 final size:34
Alignment explanation
Indices: 20953--21015 Score: 80
Period size: 31 Copynumber: 2.0 Consensus size: 34
20943 AAATGTAAAA
* *
20953 TATAAACAACTATTAATATATTTAATATATTAAG
1 TATAAACAACTATTAATAAATTAAATATATTAAG
20987 TATAAA-AA-TATT-ATAAATTAAAT-TATTAA
1 TATAAACAACTATTAATAAATTAAATATATTAA
21016 AAAAATTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.22
31 9 0.33
32 4 0.15
33 2 0.07
34 6 0.22
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (34 bp):
TATAAACAACTATTAATAAATTAAATATATTAAG
Found at i:22065 original size:31 final size:31
Alignment explanation
Indices: 22002--22168 Score: 239
Period size: 31 Copynumber: 5.5 Consensus size: 31
21992 ACGAAATAAG
* * *
22002 TAAATGATATAATCAAATT-A-ATTTGTCAT
1 TAAATGATGTAATCCAATTCATTTTTGTCAT
*
22031 TAAATGATGTAATCCAATTCATTTTTTTCAT
1 TAAATGATGTAATCCAATTCATTTTTGTCAT
*
22062 TAAATGATGCAATCCAATTCATTTTTGTCAT
1 TAAATGATGTAATCCAATTCATTTTTGTCAT
* *
22093 TAAATGATGCAATCCATTTCATTTTTGTCAT
1 TAAATGATGTAATCCAATTCATTTTTGTCAT
*
22124 TAAATGGTGTAATCCAATTCATTTTTGTCAT
1 TAAATGATGTAATCCAATTCATTTTTGTCAT
*
22155 TAAATGATATAATC
1 TAAATGATGTAATC
22169 AGTAAATGAT
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
29 17 0.14
30 1 0.01
31 106 0.85
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.44
Consensus pattern (31 bp):
TAAATGATGTAATCCAATTCATTTTTGTCAT
Found at i:23186 original size:52 final size:52
Alignment explanation
Indices: 23076--23192 Score: 128
Period size: 52 Copynumber: 2.2 Consensus size: 52
23066 GTACAAATAA
*** * *
23076 AATTTCAGGGTGGGTACCATCCGTAAAACAAGTAACTAATCGAAGAAAGCTC
1 AATTTCAGGGTGGGTACCAAAAGTAAAACAAATAACTAATCGAAGAAAACTC
* * *
23128 AGATTTCAGGGTGGG-ACCAAAAGTGAAATAAATAACTAATCGAAGAAAATTC
1 A-ATTTCAGGGTGGGTACCAAAAGTAAAACAAATAACTAATCGAAGAAAACTC
*
23180 GAATTTCAAGGTG
1 -AATTTCAGGGTG
23193 AACACGTGCC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 40 0.74
53 14 0.26
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (52 bp):
AATTTCAGGGTGGGTACCAAAAGTAAAACAAATAACTAATCGAAGAAAACTC
Found at i:23235 original size:14 final size:14
Alignment explanation
Indices: 23216--23246 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
23206 CTTCACCAAG
23216 TTGTGACTCCGCCA
1 TTGTGACTCCGCCA
23230 TTGTGACTCCGCCA
1 TTGTGACTCCGCCA
23244 TTG
1 TTG
23247 ACGAACACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.32, G:0.23, T:0.32
Consensus pattern (14 bp):
TTGTGACTCCGCCA
Found at i:27866 original size:19 final size:20
Alignment explanation
Indices: 27842--27891 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
27832 TAAGTTTAAA
*
27842 TATAATTTAAAAATATATT-
1 TATAATTTAAAAATAAATTG
27861 TATAATTTCAAAAATAAATTG
1 TATAATTT-AAAAATAAATTG
*
27882 TGTAATTTAA
1 TATAATTTAA
27892 TATATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 8 0.30
20 12 0.44
21 7 0.26
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
TATAATTTAAAAATAAATTG
Found at i:32410 original size:2 final size:2
Alignment explanation
Indices: 32403--32428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
32393 GAAATGAATA
32403 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
32429 TGACTTAATG
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:35019 original size:2 final size:2
Alignment explanation
Indices: 35012--35037 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35002 ACATACATAC
35012 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
35038 TAAGCAAAAC
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:35730 original size:20 final size:20
Alignment explanation
Indices: 35686--36113 Score: 404
Period size: 20 Copynumber: 21.2 Consensus size: 20
35676 AATGACCAAC
*
35686 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
35705 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
35725 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
35745 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
35765 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
35786 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
35807 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
35828 AAGAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
35849 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
35871 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
35889 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
35909 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
35931 --AATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
35949 AAAATCGCAACACGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
35971 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
35989 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
36011 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
36029 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
36051 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
36071 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
*
36089 AAAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
36109 AAAAT
1 AAAAT
36114 GAGTAAATTC
Statistics
Matches: 349, Mismatches: 29, Indels: 61
0.79 0.07 0.14
Matches are distributed among these distances:
18 15 0.04
19 15 0.04
20 262 0.75
21 14 0.04
22 43 0.12
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:36220 original size:6 final size:6
Alignment explanation
Indices: 36209--36253 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
36199 GACACGTATT
36209 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
36254 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:36770 original size:6 final size:6
Alignment explanation
Indices: 36759--36785 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
36749 TCTCGTCTCG
36759 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
36786 AATACGTGTC
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:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:36913 original size:20 final size:20
Alignment explanation
Indices: 36888--37087 Score: 273
Period size: 20 Copynumber: 9.8 Consensus size: 20
36878 CTCATTTTCT
36888 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
36908 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
36929 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
36948 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
36968 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
36988 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
37008 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
37028 GAAGATCGCGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
37050 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
37070 GAATATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
37088 TTCTTTTGAC
Statistics
Matches: 162, Mismatches: 6, Indels: 22
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.03
19 3 0.02
20 114 0.70
21 5 0.03
22 34 0.21
23 1 0.01
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.36
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:36936 original size:40 final size:40
Alignment explanation
Indices: 36881--37168 Score: 320
Period size: 40 Copynumber: 7.1 Consensus size: 40
36871 GAATTTACTC
*
36881 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
36921 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
36961 A--TTCTTGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTTGGAATCGCGTTGCG
*
37001 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* *
37043 ATTCTCTTAATCGCATTGCGATTCTTGGAATATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
* **** *
37085 ATTTTCTT--TTGACCGTTGCGATT-TTCTTTTCAACGTTGCG
1 ATTTTCTTAATCG--CGTTGCGATTCTTGGAATC-GCGTTGCG
* * *
37125 ATTTTCTAAATCGCGTTGCGATT-TT-TATTTCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGA-ATCGCGTTGCG
37164 ATTTT
1 ATTTT
37169 GTTGGTCATT
Statistics
Matches: 218, Mismatches: 18, Indels: 25
0.84 0.07 0.10
Matches are distributed among these distances:
38 5 0.02
39 15 0.07
40 124 0.57
41 3 0.01
42 71 0.33
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:37141 original size:20 final size:20
Alignment explanation
Indices: 36881--37168 Score: 222
Period size: 20 Copynumber: 14.2 Consensus size: 20
36871 GAATTTACTC
36881 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
36901 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
36921 ATTTTCTTAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
36941 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
36961 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
*
36981 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTGAATCGCGTTGCG
37001 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
37021 ATTCTT-GGAAGATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
* * *
37043 ATTCTCTTAATCGCATTGCG
1 ATTTTCTGAATCGCGTTGCG
*
37063 ATTCTT-GGAATATCGCGTTGCG
1 ATT-TTCTG-A-ATCGCGTTGCG
37085 ATTTTCTTTTG-A-C-CGTTGCG
1 ATTTTC---TGAATCGCGTTGCG
** *
37105 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTGAATC-GCGTTGCG
*
37125 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTGAATCGCGTTGCG
*
37145 ATTTT-T-ATTTCGCGTTGCG
1 ATTTTCTGA-ATCGCGTTGCG
37164 ATTTT
1 ATTTT
37169 GTTGGTCATT
Statistics
Matches: 226, Mismatches: 21, Indels: 43
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.00
18 2 0.01
19 20 0.09
20 158 0.70
21 16 0.07
22 28 0.12
25 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (20 bp):
ATTTTCTGAATCGCGTTGCG
Found at i:37335 original size:40 final size:39
Alignment explanation
Indices: 37301--37376 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 39
37291 TCAATGCCAA
*
37301 CAACATTATAAATAAAAATCAATAATGAACTCAATAAGTC
1 CAACATTATAAATAAAAATCAATAATGAACTCAAT-AGCC
37341 CAACATTATAAATAAAAATCAATAATGAACTCAATA
1 CAACATTATAAATAAAAATCAATAATGAACTCAATA
37377 TTTCATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
39 1 0.03
40 35 0.97
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.25
Consensus pattern (39 bp):
CAACATTATAAATAAAAATCAATAATGAACTCAATAGCC
Found at i:42141 original size:25 final size:25
Alignment explanation
Indices: 42096--42144 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
42086 TAATAAGTTA
*
42096 ATATAAAAATATTTTTAAATTTAAC
1 ATATAAAAATATTTATAAATTTAAC
*
42121 ATATAAAAA-ATATTATGAATTTAA
1 ATATAAAAATAT-TTATAAATTTAA
42145 TTATTTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
ATATAAAAATATTTATAAATTTAAC
Found at i:45550 original size:24 final size:24
Alignment explanation
Indices: 45515--45574 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
45505 GGTACTGGTG
45515 ATTAG-TTAGAGCAGAACACAACA
1 ATTAGTTTAGAGCAGAACACAACA
45538 ATTAGTTTAGAGCAGAACACAACA
1 ATTAGTTTAGAGCAGAACACAACA
45562 ATTAGTTTAGAGC
1 ATTAGTTTAGAGC
45575 TTGCACAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 5 0.14
24 31 0.86
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.23
Consensus pattern (24 bp):
ATTAGTTTAGAGCAGAACACAACA
Found at i:45843 original size:12 final size:12
Alignment explanation
Indices: 45819--45877 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 12
45809 GTTAGTGGAA
*
45819 TTTAATTTATTT
1 TTTATTTTATTT
*
45831 TTTATTTTGTTTT
1 TTTATTTT-ATTT
*
45844 GTTTTTCTTTATTT
1 -TTTAT-TTTATTT
45858 ATTTATTTTATTT
1 -TTTATTTTATTT
45871 TTTATTT
1 TTTATTT
45878 GTCTTTTTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 14 0.37
13 10 0.26
14 11 0.29
15 3 0.08
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:45924 original size:24 final size:24
Alignment explanation
Indices: 45855--45956 Score: 63
Period size: 24 Copynumber: 4.3 Consensus size: 24
45845 TTTTTCTTTA
*
45855 TTTATTTAT-TTTATTTT-TTATT
1 TTTATTTATCTATATTTTATTATT
* *
45877 TGTCTTTTTA-CTA-AATTTATTTATT
1 T-T-TATTTATCTATATTTTA-TTATT
45902 TTTATTTATCTATATTTTATTATT
1 TTTATTTATCTATATTTTATTATT
* * *
45926 GTTATATTAAC-ATTTTTTTATTA-T
1 TTTAT-TTATCTA-TATTTTATTATT
45950 TTTATTT
1 TTTATTT
45957 TTTCTAACAT
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
22 1 0.02
23 12 0.19
24 25 0.40
25 24 0.39
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTATTTATCTATATTTTATTATT
Found at i:46038 original size:13 final size:13
Alignment explanation
Indices: 46020--46048 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
46010 GAATCGGGTT
46020 TTTAAATTTCAAA
1 TTTAAATTTCAAA
46033 TTTAAATTTCAAA
1 TTTAAATTTCAAA
46046 TTT
1 TTT
46049 TCGCAATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAAATTTCAAA
Found at i:50119 original size:37 final size:34
Alignment explanation
Indices: 50072--50200 Score: 141
Period size: 36 Copynumber: 3.6 Consensus size: 34
50062 ACAAAGGGTC
* *
50072 GTCTCGCTTGAGACTAATTTACTCAAAACAAAGTTTT
1 GTCTCTCTTGAGAC-AGTTT-CTCAAAACAAA-TTTT
* *
50109 ATCTCTCTTGAGACAGTTTCTCTTTAAACAAATTTT
1 GTCTCTCTTGAGACAGTTTCTC--AAAACAAATTTT
**
50145 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTT
1 GTCTCTCTTGAGACAGTTT--CTCAAAACAAATTTT
50181 GTCTCTCTTGAGACAGTTTC
1 GTCTCTCTTGAGACAGTTTC
50201 CCTTGAAACA
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
34 1 0.01
35 3 0.04
36 56 0.69
37 19 0.23
38 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (34 bp):
GTCTCTCTTGAGACAGTTTCTCAAAACAAATTTT
Found at i:50157 original size:36 final size:36
Alignment explanation
Indices: 50097--50493 Score: 319
Period size: 36 Copynumber: 11.2 Consensus size: 36
50087 AATTTACTCA
* *
50097 AAACAAAGTTTTATCTCTCTTGAGACAGTTTCTCTTT
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
50134 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
50170 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
50206 AAACAAA------ATCT-TTGA-ATATGTTT-TCCTTT
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCT-CTTG
* * * *
50235 AAACAAATTTCGTCTCCCTTAAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
50271 AAATAAATTTTGTCTCTCTAGAGACAGTTTCTCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* *
50307 AAACAAA------ATCT-TTGA-ATATGTTT-TACATT-
1 AAACAAATTTTGTCTCTCTTGAGACA-GTTTCT-C-TTG
* * * * *
50336 AAACAAATTTCGTCTCCCTTGAGATAGCTTCTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
* * *
50372 GAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
*
50409 AAACAAATTTTGTCTTTGTCTCTCTTGAGACAGATTCTCTTG
1 AAACAAA-----T-TTTGTCTCTCTTGAGACAGTTTCTCTTG
*
50451 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
50487 AAACAAA
1 AAACAAA
50494 ATATTTGAAT
Statistics
Matches: 288, Mismatches: 41, Indels: 63
0.73 0.10 0.16
Matches are distributed among these distances:
28 5 0.02
29 33 0.11
30 8 0.03
35 6 0.02
36 160 0.56
37 42 0.15
41 1 0.00
42 33 0.11
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTG
Found at i:50307 original size:101 final size:101
Alignment explanation
Indices: 50125--50415 Score: 438
Period size: 101 Copynumber: 2.9 Consensus size: 101
50115 CTTGAGACAG
* * *
50125 TTTCTCTTTAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTT
1 TTTC-CTTTAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTT
50190 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
65 GAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
* *
50227 TTTCCTTTAAACAAATTTCGTCTCCCTTAAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTAG
1 TTTCCTTTAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTG
*
50292 AGACAGTTTCTCTTGAAACAAAATCTTTGAATATGT
66 AGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
* * * * ** * *
50328 TTTACATTAAACAAATTTCGTCTCCCTTGAGATAGCTTCTTTTGGAACTAAGTTTTGTCTCTCTT
1 TTTCCTTTAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTCTCTCTT
50393 GAGACAGTTTCCCTTGAAACAAA
65 GAGACAGTTTCCCTTGAAACAAA
50416 TTTTGTCTTT
Statistics
Matches: 171, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
101 127 0.74
102 44 0.26
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (101 bp):
TTTCCTTTAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAATAAATTTTGTCTCTCTTG
AGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
Found at i:50469 original size:78 final size:79
Alignment explanation
Indices: 50347--50493 Score: 233
Period size: 78 Copynumber: 1.9 Consensus size: 79
50337 AACAAATTTC
* * * * *
50347 GTCTCCCTTGAGATAGCTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTCTCCCTTGAGACAGATTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
50412 CAAATTTTGTCTTT
66 CAAATTTTGTCTTT
*
50426 GTCTCTCTTGAGACAGATTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
1 GTCTCCCTTGAGACAGATTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
50490 CAAA
66 CAAA
50494 ATATTTGAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 38 0.61
79 24 0.39
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (79 bp):
GTCTCCCTTGAGACAGATTCTCTTGAAACTAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA
CAAATTTTGTCTTT
Found at i:50589 original size:36 final size:36
Alignment explanation
Indices: 50516--50659 Score: 182
Period size: 36 Copynumber: 4.0 Consensus size: 36
50506 GTTTTCCTTG
* * *
50516 TTTTGTCTTTCTTGAGACTGTTTCTCTCGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
* * * *
50552 TTTTATCTCTCTTAAGACAATTTCTCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
* * *
50588 TTTTGTCTCTCTTGAGATAGTTTCTTTTTAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
50624 TTTTGTCTCTCTTGAGACAGTTTACT-TTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTT-CTCTTGAAACAAA
50660 ATCTTTGAGT
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
36 89 0.98
37 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
Found at i:52495 original size:14 final size:15
Alignment explanation
Indices: 52478--52560 Score: 50
Period size: 14 Copynumber: 5.7 Consensus size: 15
52468 TGGAATTTAA
52478 TTTAATTTATTTTT-
1 TTTAATTTATTTTTC
* *
52492 TTTATTTTGTTTTTC
1 TTTAATTTATTTTTC
52507 TTT-ATTTA--TTTC
1 TTTAATTTATTTTTC
*
52519 TTTATTTTTATTTTTAC
1 TTTA-ATTTATTTTT-C
* *
52536 -TAAATTTATTTATC
1 TTTAATTTATTTTTC
* *
52550 TATATTTTATT
1 TTTAATTTATT
52561 ATTTTTATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 13
0.68 0.15 0.17
Matches are distributed among these distances:
12 7 0.14
14 20 0.39
15 18 0.35
16 5 0.10
17 1 0.02
ACGTcount: A:0.20, C:0.05, G:0.01, T:0.73
Consensus pattern (15 bp):
TTTAATTTATTTTTC
Found at i:56255 original size:17 final size:18
Alignment explanation
Indices: 56233--56266 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56223 TTGAAAGGTC
*
56233 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
56250 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
56267 ACAAAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:57216 original size:31 final size:31
Alignment explanation
Indices: 57118--57208 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
57108 CAATTTAAGG
57118 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
57149 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
57180 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
57209 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:57452 original size:21 final size:21
Alignment explanation
Indices: 57426--57467 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
57416 ATTTGAATAT
*
57426 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
57447 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
57468 CTCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:57529 original size:21 final size:21
Alignment explanation
Indices: 57496--57535 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
57486 TTTTTGTAGA
*
57496 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
57518 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
57536 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:57788 original size:34 final size:32
Alignment explanation
Indices: 57749--57818 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
57739 TTTTGTAAAG
*
57749 GGGAAAAGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
57783 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
57815 GGGA
1 GGGA
57819 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:58387 original size:12 final size:12
Alignment explanation
Indices: 58372--58441 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
58362 GATACATGAC
*
58372 CTGAATTTTGTT
1 CTGAATTCTGTT
* * *
58384 CTGATTTTTGAT
1 CTGAATTCTGTT
*
58396 CTGGATTCTGTT
1 CTGAATTCTGTT
*
58408 ATG-ATATCTGTT
1 CTGAAT-TCTGTT
58420 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
58432 TTGATTTCTG
1 CTGAATTCTG
58442 ATATATCCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.54
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:58407 original size:24 final size:24
Alignment explanation
Indices: 58349--58443 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
58339 ATTTCCGACT
*
58349 TGAATTCTGTTCTGATA-CATGACC
1 TGAATTCTGTTCTGATATC-TGATC
* * *
58373 TGAATTTTGTTCTGATTTTTGATC
1 TGAATTCTGTTCTGATATCTGATC
* * *
58397 TGGATTCTGTTATGATATCTGTTC
1 TGAATTCTGTTCTGATATCTGATC
* *
58421 TGAATTCTGTTTTGATTTCTGAT
1 TGAATTCTGTTCTGATATCTGAT
58444 ATATCCGTTT
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.19, C:0.13, G:0.18, T:0.51
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATC
Found at i:59703 original size:27 final size:25
Alignment explanation
Indices: 59640--59703 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
59630 AAAAAGATGA
*
59640 AAAAATATATTTTAAAAATATTTAAT
1 AAAAATAT-TTTGAAAAATATTTAAT
*
59666 -CAAATATTTTTGAAATATATATTTAAT
1 AAAAATA-TTTTGAAA-A-ATATTTAAT
59693 AAAAATATTTT
1 AAAAATATTTT
59704 TTAATGTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 11 0.35
26 2 0.06
27 13 0.42
28 5 0.16
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAAATATTTTGAAAAATATTTAAT
Found at i:59900 original size:25 final size:27
Alignment explanation
Indices: 59862--59930 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 27
59852 ATTATATATA
*
59862 TTAACTTAAAATATTTTTA-TATTAAC
1 TTAATTTAAAATATTTTTATTATTAAC
59888 TT-A-TT-AAATATATTTTATTATTAAC
1 TTAATTTAAAATAT-TTTTATTATTAAC
59913 TTAATTTAAAAATATTTT
1 TTAATTT-AAAATATTTT
59931 ATTTTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
23 6 0.16
24 7 0.19
25 10 0.27
26 3 0.08
27 2 0.05
28 3 0.08
29 6 0.16
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAATTTAAAATATTTTTATTATTAAC
Found at i:59921 original size:27 final size:25
Alignment explanation
Indices: 59850--59933 Score: 95
Period size: 27 Copynumber: 3.4 Consensus size: 25
59840 TATATTCATA
*
59850 ATATTATATATATTAACTTA--AAAT
1 ATATTTTAT-TATTAACTTATTAAAT
59874 AT-TTTTA-TATTAACTTATTAAAT
1 ATATTTTATTATTAACTTATTAAAT
*
59897 ATATTTTATTATTAACTTAATTTAAAA
1 ATATTTTATTATTAACTT-A-TTAAAT
59924 ATATTTTATT
1 ATATTTTATT
59934 TTTATTTAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.19
23 10 0.19
24 7 0.13
25 9 0.17
26 1 0.02
27 15 0.29
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
ATATTTTATTATTAACTTATTAAAT
Found at i:59953 original size:20 final size:21
Alignment explanation
Indices: 59916--59955 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
59906 TATTAACTTA
*
59916 ATTTAAAAATATTTTATTTTT
1 ATTTAAAAATATTATATTTTT
*
59937 ATTTAAAATTA-TATATTTT
1 ATTTAAAAATATTATATTTT
59956 GTTAAAATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTAAAAATATTATATTTTT
Found at i:64102 original size:26 final size:26
Alignment explanation
Indices: 64050--64154 Score: 78
Period size: 24 Copynumber: 4.1 Consensus size: 26
64040 TATCTTAATG
* *
64050 TATAAATACTTAAATTCATAATATTT
1 TATATATACTTAAATTCAAAATATTT
*
64076 TATATATA-TTAACTTCAAAATATTT
1 TATATATACTTAAATTCAAAATATTT
*
64101 T-TATATTAACTT--ATT-AATATATTT
1 TATATA-T-ACTTAAATTCAAAATATTT
* *
64125 TAT-TATTAACTTAATTTAAAAATATTT
1 TATATA-T-ACTTAAATTCAAAATATTT
64152 TAT
1 TAT
64155 TTTTATTTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
24 22 0.34
25 20 0.31
26 10 0.15
27 13 0.20
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (26 bp):
TATATATACTTAAATTCAAAATATTT
Found at i:64108 original size:22 final size:23
Alignment explanation
Indices: 64080--64137 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 23
64070 ATATTTTATA
64080 TATATTAACTTCA-AAATAT-TTT
1 TATATTAACTT-ATAAATATATTT
*
64102 TATATTAACTTATTAATATATTT
1 TATATTAACTTATAAATATATTT
64125 TATTATTAACTTA
1 TA-TATTAACTTA
64138 ATTTAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 1 0.03
22 16 0.50
23 5 0.16
24 10 0.31
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (23 bp):
TATATTAACTTATAAATATATTT
Found at i:64345 original size:31 final size:31
Alignment explanation
Indices: 64305--64366 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
64295 ACCAATGATA
*
64305 ATCACATCTTAATTAAATAAAAATGAAAGTG
1 ATCACATCTTAATTAAATAAAAACGAAAGTG
* *
64336 ATCATATCTTAATTAAATAAACACGAAAGTG
1 ATCACATCTTAATTAAATAAAAACGAAAGTG
64367 GTCGTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.29
Consensus pattern (31 bp):
ATCACATCTTAATTAAATAAAAACGAAAGTG
Found at i:65612 original size:21 final size:21
Alignment explanation
Indices: 65586--65634 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
65576 AGATAACATG
65586 GTGTATATATTTTGCATCTTA
1 GTGTATATATTTTGCATCTTA
* *
65607 GTGTATATATTTTGTATTTTA
1 GTGTATATATTTTGCATCTTA
65628 GTGTATA
1 GTGTATA
65635 AATGCTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.16, T:0.55
Consensus pattern (21 bp):
GTGTATATATTTTGCATCTTA
Found at i:65668 original size:25 final size:23
Alignment explanation
Indices: 65640--65686 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
65630 GTATAAATGC
65640 TTAAATTCATAATATTTTATATATA
1 TTAAATTCA-AATATTTT-TATATA
* *
65665 TTAACTTTAAATATTTTTATAT
1 TTAAATTCAAATATTTTTATAT
65687 TAACTTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 8 0.40
25 7 0.35
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAATTCAAATATTTTTATATA
Found at i:65687 original size:21 final size:23
Alignment explanation
Indices: 65661--65719 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 23
65651 ATATTTTATA
65661 TATATTAACTTTAAATAT-T-TT
1 TATATTAACTTTAAATATATATT
65682 TATATTAACTTATTAAATATATATT
1 TATATTAAC-T-TTAAATATATATT
*
65707 TTTATTAA-TTTAA
1 TATATTAACTTTAA
65720 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 9 0.27
22 5 0.15
23 9 0.27
24 1 0.03
25 9 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
TATATTAACTTTAAATATATATT
Found at i:65732 original size:15 final size:15
Alignment explanation
Indices: 65714--65753 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
65704 ATTTTTATTA
*
65714 ATTTAATTTTAAAAT
1 ATTTTATTTTAAAAT
65729 ATTTTATTTTAAAAT
1 ATTTTATTTTAAAAT
65744 ATTTTATTTT
1 ATTTTATTTT
65754 CATTTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTATTTTAAAAT
Found at i:65758 original size:21 final size:19
Alignment explanation
Indices: 65727--65783 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
65717 TAATTTTAAA
65727 ATATTTTATTTTAAAATATT
1 ATATTTTATTTTAAAATA-T
* *
65747 TTATTTTCATTTAAAAATAT
1 ATATTTT-ATTTTAAAATAT
*
65767 ATATTTTATGTTAAAAT
1 ATATTTTATTTTAAAAT
65784 TGATTTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 8 0.26
20 13 0.42
21 10 0.32
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATATTTTATTTTAAAATAT
Found at i:65945 original size:31 final size:31
Alignment explanation
Indices: 65907--65974 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
65897 TGATGACTAC
*
65907 ATCTTAATTAAATAAAAACAAAAGTGACCTT
1 ATCTTAATTAAATAAAAACAAAAGTGACCAT
* ** *
65938 ATCTTAATTAAGTAAAAATGAAAGTGATCAT
1 ATCTTAATTAAATAAAAACAAAAGTGACCAT
65969 ATCTTA
1 ATCTTA
65975 TATTTTTTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.32
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGACCAT
Found at i:67173 original size:129 final size:129
Alignment explanation
Indices: 66934--67179 Score: 370
Period size: 129 Copynumber: 1.9 Consensus size: 129
66924 ATTGATTATC
* * *
66934 ATTGGTTGCACACTTTTCAGTGTACCTATGATGCTCAGTAACACCAATGCTTACACAAGTATATA
1 ATTGGTTGCACACTTTTCAGTGTACCGATGATACTCAGCAACACCAATGCTTACACAAGTATATA
*
66999 GCAACTCGAATAAAACTTCATCTAGATTTAAAAAAAATATATATATATGTAACAATATTAATCA
66 ACAACTCGAATAAAACTTCATCTAGATTTAAAAAAAATATATATATATGTAACAATATTAATCA
* * *
67063 ATTGGTTGCACACTTTTTAGTGTACCGATGCTACTTAGCAACACCAATGCTTACACAAGTATATA
1 ATTGGTTGCACACTTTTCAGTGTACCGATGATACTCAGCAACACCAATGCTTACACAAGTATATA
* * *
67128 ATAACTCGAATAAAA-TTACTTCTATATTTAAACAAAAATAT-TATATATGTAA
66 ACAACTCGAATAAAACTT-CATCTAGATTTAAA-AAAAATATATATATATGTAA
67180 TTACAAATAT
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
128 2 0.02
129 95 0.90
130 8 0.08
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (129 bp):
ATTGGTTGCACACTTTTCAGTGTACCGATGATACTCAGCAACACCAATGCTTACACAAGTATATA
ACAACTCGAATAAAACTTCATCTAGATTTAAAAAAAATATATATATATGTAACAATATTAATCA
Found at i:71091 original size:2 final size:2
Alignment explanation
Indices: 71086--71111 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71076 AATACAATTA
71086 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
71112 CCTTTATTAT
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:71142 original size:10 final size:10
Alignment explanation
Indices: 71089--71143 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
71079 ACAATTAATA
71089 TATA-TATAT
1 TATACTATAT
71098 ATATA-TATAT
1 -TATACTATAT
* *
71108 ATATCCTTTAT
1 -TATACTATAT
71119 TATACTAT-T
1 TATACTATAT
71128 TATACTATAT
1 TATACTATAT
71138 TATACT
1 TATACT
71144 TAATATAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 9 0.23
10 26 0.67
11 4 0.10
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (10 bp):
TATACTATAT
Found at i:72762 original size:50 final size:50
Alignment explanation
Indices: 72664--72848 Score: 232
Period size: 50 Copynumber: 3.7 Consensus size: 50
72654 AATTTATATT
* * **
72664 ATAAAAAA-TGTAACACTTAATACATACGTACATTGATGTAAGTAAATAAA
1 ATAAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAGT-AATAAA
* * ** *
72714 ATAAATAAGTATAGTACTTAATACATAC-TACA-CGAGTGTAAGTGAATAAA
1 ATAAAAAAGTGTAACACTTAACACATACTTACACCGA-TGTAAGT-AATAAA
72764 ATAAAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAGTAATAAA
1 AT-AAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAGTAATAAA
72815 ATAAAAAAGTGTAACACTTAACACATACTTACAC
1 ATAAAAAAGTGTAACACTTAACACATACTTACAC
72849 TTTTAGTATC
Statistics
Matches: 119, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
49 2 0.02
50 58 0.49
51 45 0.38
52 11 0.09
53 3 0.03
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (50 bp):
ATAAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAGTAATAAA
Found at i:72848 original size:102 final size:101
Alignment explanation
Indices: 72666--72848 Score: 260
Period size: 102 Copynumber: 1.8 Consensus size: 101
72656 TTTATATTAT
* ** * **
72666 AAAAAATGTAACACTTAATACATACGTACATTGATGTAAGTAAATAAAATAAATAAGTATAGTAC
1 AAAAAATGTAACACTTAACACATACGTACACCGATGTAAGTAAATAAAATAAAAAAGTATAACAC
*
72731 TTAATACATACTACACGAGTGTAAGTGAATAAAATA
66 TTAACACATACTACACGAGTGTAAGTGAATAAAATA
* *
72767 AAAAAAGTGTAACACTTAACACATACTTACACCGATGTAAGT-AATAAAATAAAAAAGTGTAACA
1 AAAAAA-TGTAACACTTAACACATACGTACACCGATGTAAGTAAATAAAATAAAAAAGTATAACA
72831 CTTAACACATACTTACAC
65 CTTAACACATAC-TACAC
72849 TTTTAGTATC
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
101 35 0.49
102 36 0.51
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (101 bp):
AAAAAATGTAACACTTAACACATACGTACACCGATGTAAGTAAATAAAATAAAAAAGTATAACAC
TTAACACATACTACACGAGTGTAAGTGAATAAAATA
Done.