Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000071.1 Hibiscus syriacus cultivar Beakdansim tig00000125_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: 126842
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:7387 original size:34 final size:36
Alignment explanation
Indices: 7344--7410 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
7334 CAAAACAACA
* *
7344 GTTCGAAAAA-AAGAAAAAAAAGA-AAAAAAGAGAT
1 GTTCAAAAAAGAAAAAAAAAAAGAGAAAAAAGAGAT
7378 GTTCAAAAAAGAAAAAAAAAAAGAGAAAAAAGA
1 GTTCAAAAAAGAAAAAAAAAAAGAGAAAAAAGA
7411 CATAAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 9 0.31
35 12 0.41
36 8 0.28
ACGTcount: A:0.73, C:0.03, G:0.16, T:0.07
Consensus pattern (36 bp):
GTTCAAAAAAGAAAAAAAAAAAGAGAAAAAAGAGAT
Found at i:11362 original size:23 final size:23
Alignment explanation
Indices: 11336--11385 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
11326 AAAACTTCAG
11336 CCATGGCTTTTCGAATCCGAACA
1 CCATGGCTTTTCGAATCCGAACA
11359 CCATGGCTTTTCGAATCCGAACA
1 CCATGGCTTTTCGAATCCGAACA
11382 CCAT
1 CCAT
11386 TGGAACTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (23 bp):
CCATGGCTTTTCGAATCCGAACA
Found at i:13164 original size:15 final size:17
Alignment explanation
Indices: 13133--13164 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
13123 CGGTGGGATT
13133 TGAGACATATCAGAATC
1 TGAGACATATCAGAATC
13150 TGAGA-ATAT-AGAATC
1 TGAGACATATCAGAATC
13165 AGTGTAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (17 bp):
TGAGACATATCAGAATC
Found at i:34708 original size:17 final size:17
Alignment explanation
Indices: 34675--34708 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
34665 GACTCTTTTT
* *
34675 CATAAATAAATATATTA
1 CATAAATAAAAAAATTA
34692 CATAAATAAAAAAATTA
1 CATAAATAAAAAAATTA
34709 AGAAAACATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
CATAAATAAAAAAATTA
Found at i:35914 original size:2 final size:2
Alignment explanation
Indices: 35907--35952 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
35897 CTCATGGATG
35907 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
35949 AT AT
1 AT AT
35953 TCACCTATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36029 original size:26 final size:28
Alignment explanation
Indices: 35999--36054 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
35989 ATTATAATTA
*
35999 TAAAATATAATAATT-AAT-ATTATTTT
1 TAAAATATAATAATTCAATCAATATTTT
*
36025 TAAAATATTATAATTCAATCAATATTTT
1 TAAAATATAATAATTCAATCAATATTTT
36053 TA
1 TA
36055 TGAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 14 0.54
27 3 0.12
28 9 0.35
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (28 bp):
TAAAATATAATAATTCAATCAATATTTT
Found at i:40475 original size:412 final size:412
Alignment explanation
Indices: 39711--40530 Score: 1631
Period size: 412 Copynumber: 2.0 Consensus size: 412
39701 TGCAAGCAAG
*
39711 ATTGAAACACGGAAAGGAATCATGAAAGTGTTCCGTGGAGCGCTTGTGGTACTGAAAGGCGAAAA
1 ATTGAAACACGGAAAGGAATCATGAAAGTGTTCCGTGAAGCGCTTGTGGTACTGAAAGGCGAAAA
39776 AATAGCTGCAAACTTGTACATGCTGAAGGGAGAGACTTTGGTAGAAGCAGAAGCCTCTGTTGCCT
66 AATAGCTGCAAACTTGTACATGCTGAAGGGAGAGACTTTGGTAGAAGCAGAAGCCTCTGTTGCCT
39841 CATGTAGTTCAGATTCGGCAATGCTATGGCATCAGAAACTTGGACACATGTCAGAACAAGGAATG
131 CATGTAGTTCAGATTCGGCAATGCTATGGCATCAGAAACTTGGACACATGTCAGAACAAGGAATG
39906 AAAGTCCTTGTGGAGCAAAAGCTACTTCCAGGCTTAACAAAGGTATCACTTCCTTTGTGTGAGCA
196 AAAGTCCTTGTGGAGCAAAAGCTACTTCCAGGCTTAACAAAGGTATCACTTCCTTTGTGTGAGCA
39971 TTGCATAACAAGTAAGCAACACCGGTTGAAATTCAACACATCAAATTCTAGAGGCAAAAGTGTTC
261 TTGCATAACAAGTAAGCAACACCGGTTGAAATTCAACACATCAAATTCTAGAGGCAAAAGTGTTC
40036 TAGAATTGGTTCACTCTGACGTATGGAAAGCACCAGTAACGTCCCTAGGTGGAGCAAAATACTTT
326 TAGAATTGGTTCACTCTGACGTATGGAAAGCACCAGTAACGTCCCTAGGTGGAGCAAAATACTTT
40101 GTCTCATTTATTGATGACCAAT
391 GTCTCATTTATTGATGACCAAT
40123 ATTGAAACACGGAAAGGAATCATGAAAGTGTTCCGTGAAGCGCTTGTGGTACTGAAAGGCGAAAA
1 ATTGAAACACGGAAAGGAATCATGAAAGTGTTCCGTGAAGCGCTTGTGGTACTGAAAGGCGAAAA
40188 AATAGCTGCAAACTTGTACATGCTGAAGGGAGAGACTTTGGTAGAAGCAGAAGCCTCTGTTGCCT
66 AATAGCTGCAAACTTGTACATGCTGAAGGGAGAGACTTTGGTAGAAGCAGAAGCCTCTGTTGCCT
40253 CATGTAGTTCAGATTCGGCAATGCTATGGCATCAGAAACTTGGACACATGTCAGAACAAGGAATG
131 CATGTAGTTCAGATTCGGCAATGCTATGGCATCAGAAACTTGGACACATGTCAGAACAAGGAATG
40318 AAAGTCCTTGTGGAGCAAAAGCTACTTCCAGGCTTAACAAAGGTATCACTTCCTTTGTGTGAGCA
196 AAAGTCCTTGTGGAGCAAAAGCTACTTCCAGGCTTAACAAAGGTATCACTTCCTTTGTGTGAGCA
40383 TTGCATAACAAGTAAGCAACACCGGTTGAAATTCAACACATCAAATTCTAGAGGCAAAAGTGTTC
261 TTGCATAACAAGTAAGCAACACCGGTTGAAATTCAACACATCAAATTCTAGAGGCAAAAGTGTTC
40448 TAGAATTGGTTCACTCTGACGTATGGAAAGCACCAGTAACGTCCCTAGGTGGAGCAAAATACTTT
326 TAGAATTGGTTCACTCTGACGTATGGAAAGCACCAGTAACGTCCCTAGGTGGAGCAAAATACTTT
40513 GTCTCATTTATTGATGAC
391 GTCTCATTTATTGATGAC
40531 TACTACAGGA
Statistics
Matches: 407, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
412 407 1.00
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (412 bp):
ATTGAAACACGGAAAGGAATCATGAAAGTGTTCCGTGAAGCGCTTGTGGTACTGAAAGGCGAAAA
AATAGCTGCAAACTTGTACATGCTGAAGGGAGAGACTTTGGTAGAAGCAGAAGCCTCTGTTGCCT
CATGTAGTTCAGATTCGGCAATGCTATGGCATCAGAAACTTGGACACATGTCAGAACAAGGAATG
AAAGTCCTTGTGGAGCAAAAGCTACTTCCAGGCTTAACAAAGGTATCACTTCCTTTGTGTGAGCA
TTGCATAACAAGTAAGCAACACCGGTTGAAATTCAACACATCAAATTCTAGAGGCAAAAGTGTTC
TAGAATTGGTTCACTCTGACGTATGGAAAGCACCAGTAACGTCCCTAGGTGGAGCAAAATACTTT
GTCTCATTTATTGATGACCAAT
Found at i:60487 original size:22 final size:21
Alignment explanation
Indices: 60462--60504 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
60452 TATGTTGATT
60462 TTAAAATATAAACATATAAATA
1 TTAAAATATAAACATA-AAATA
* * *
60484 TTAAGATTTAAACCTAAAATA
1 TTAAAATATAAACATAAAATA
60505 ATATCAAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
TTAAAATATAAACATAAAATA
Found at i:62180 original size:130 final size:130
Alignment explanation
Indices: 61912--62182 Score: 314
Period size: 130 Copynumber: 2.1 Consensus size: 130
61902 GGATTTGATT
* * * * * *
61912 TTCCCTAAAGAGTGGCAGAGTAGATCTCATGTCTAGATTTAATTTTCCCTGAAGAGCAGTGGAGC
1 TTCCCTAAAGAGTAGCAGAGTAGATCCCATGTCCAGATTTAATCTTACCTGAAGAGCAGTGGAAC
* * * * * * * *
61977 AAATCTACCTCGATTCAATCTTCTCCGAAAAGTAGTGAAGTGAATCAATGTCTTTAGATCTGATC
66 AAATCTACCTCGATTCAATCTTCTCCAAAAAGCAATGAAGTAAATCAAAGTCTTTAGATATAATA
* * * *
62042 TTCACTAAAGAGTAGCGGA-TCAGATCCCATGTCCAGATTTGATCTTACCTGAAGAGCATTGGAA
1 TTCCCTAAAGAGTAGCAGAGT-AGATCCCATGTCCAGATTTAATCTTACCTGAAGAGCAGTGGAA
* *
62106 CAAATCTACCTCGATTTAATCTTC-CCTAAAAAGCAATTAAGTAAATCAAAGT-TTGTAGATATA
65 CAAATCTACCTCGATTCAATCTTCTCC-AAAAAGCAATGAAGTAAATCAAAGTCTT-TAGATATA
62169 ATA
128 ATA
62172 TTCCCTAAAGA
1 TTCCCTAAAGA
62183 ATGACAACTC
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
129 5 0.04
130 112 0.96
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (130 bp):
TTCCCTAAAGAGTAGCAGAGTAGATCCCATGTCCAGATTTAATCTTACCTGAAGAGCAGTGGAAC
AAATCTACCTCGATTCAATCTTCTCCAAAAAGCAATGAAGTAAATCAAAGTCTTTAGATATAATA
Found at i:63502 original size:20 final size:20
Alignment explanation
Indices: 63466--63503 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
63456 ATCCTATTCC
**
63466 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
63486 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
63504 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:64488 original size:2 final size:2
Alignment explanation
Indices: 64481--64521 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
64471 TCTTGCATGA
64481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64522 CATTTACTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:66991 original size:96 final size:95
Alignment explanation
Indices: 66866--67088 Score: 279
Period size: 96 Copynumber: 2.3 Consensus size: 95
66856 ATCGAAAAGG
* * ** * *
66866 TAGTATTGATACCATAATAAGGGTATCGATACCACTCTACATCGAATCTAAAA-TGGGTATCGAT
1 TAGTATCGATACCATGATAAGGGTATCGATACCAAGCAACATCGAATC-AAAAGTGGGTATCAAT
* *
66930 ACTGGAA-GAGGTATCGGTACCATACTATATAA
65 ACTAGAAGGAGGTATCAGTACCATA-TA-ATAA
* * *
66962 TAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCGAATCAAAAGTTGGTATTAATA
1 TAGTATCGATACCATGATAAGGGTATCGATACCAAGCAACATCGAATCAAAAGTGGGTATCAATA
* *
67027 CTAGAAGGGGGTATCAGTACCATATAATAG
66 CTAGAAGGAGGTATCAGTACCATATAATAA
*
67057 TAGTATCGATACCATGATAGGGGTATCGATAC
1 TAGTATCGATACCATGATAAGGGTATCGATAC
67089 TATAGGGCAA
Statistics
Matches: 110, Mismatches: 15, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
95 37 0.34
96 58 0.53
97 15 0.14
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (95 bp):
TAGTATCGATACCATGATAAGGGTATCGATACCAAGCAACATCGAATCAAAAGTGGGTATCAATA
CTAGAAGGAGGTATCAGTACCATATAATAA
Found at i:67494 original size:57 final size:57
Alignment explanation
Indices: 67430--68027 Score: 916
Period size: 57 Copynumber: 10.5 Consensus size: 57
67420 GTACAAAATA
67430 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
67487 TAAGAAATCGTACTAAGTGTATGAATTTCAGATAGGGCGTTTTGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
67544 GAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
67601 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
67658 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
67715 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
67772 TAAGAAATCATAC-AAGTGTATGAATTTTAGATAGGGCGTCTCGTACGATAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * * * *
67828 TAAGAAATCATACTAAGTGTATGAATTTCTGACA-TGCGTTTTGTCCACT-AAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
67883 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGTGTTTCGTACGCTAAAATGA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* ** ** * *
67940 TAAGGAAATCATACTAAGTGTATCAATTTCCAG-TAGGGCACTTCGTGTGCTAACATGA
1 TAA-GAAATCATACTAAGTGTATGAATTT-CAGATAGGGCGTTTCGTACGCTAAAATGT
67998 TAAGAAATTCATACTAAGTGTATGAATTTC
1 TAAGAAA-TCATACTAAGTGTATGAATTTC
68028 TAAATTGGAC
Statistics
Matches: 495, Mismatches: 40, Indels: 12
0.90 0.07 0.02
Matches are distributed among these distances:
55 38 0.08
56 71 0.14
57 317 0.64
58 66 0.13
59 3 0.01
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:68729 original size:45 final size:45
Alignment explanation
Indices: 68679--68792 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
68669 GCATAATTGT
* * *
68679 ATGAAAGGATGCCATAAATGAAATATATAATAGTGTATCAAAGGC
1 ATGAAAGGATGCCATAAATGAAATATATAATAGTGAATAAAAGAC
** *
68724 ATGAAAGGATGCCATAAATGAAAGGTATAATAGTGAATAAAAGAT
1 ATGAAAGGATGCCATAAATGAAATATATAATAGTGAATAAAAGAC
* * *
68769 ATGTAAGGATGACATAATTGAAAT
1 ATGAAAGGATGCCATAAATGAAAT
68793 GCATATAGGT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.25
Consensus pattern (45 bp):
ATGAAAGGATGCCATAAATGAAATATATAATAGTGAATAAAAGAC
Found at i:70427 original size:2 final size:2
Alignment explanation
Indices: 70420--70448 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
70410 ATTAGGTCAG
70420 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
70449 CATAGTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:72233 original size:96 final size:98
Alignment explanation
Indices: 72097--72289 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 98
72087 GTTTGAATGA
* * * * *
72097 GTATCGATACCATGGTAAGGGTATCAATACTAGTCTACATCGAATCTAAAATGGGTATTGATACC
1 GTATCGATACCATGGTAAGGGTATCAATACAAGTCAACATCGAATCAAAAATGGGAATCGATACC
* * *
72162 -GGAAGGGGTATCGATACCATAATATA-TAGTG
66 AGAAAAGAGTATCGATACCATAATATAGTAGTG
* ** *
72193 GTATCGATACTATGGTAAGGGTATTGATACCAAG-CAACATCGAATCAAAAATTGGAATCGATAC
1 GTATCGATACCATGGTAAGGGTATCAATA-CAAGTCAACATCGAATCAAAAATGGGAATCGATAC
* *
72257 CATAAAAGAGTATCGGTACCATAATATAGTAGT
65 CAGAAAAGAGTATCGATACCATAATATAGTAGT
72290 ATCAATACCA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
96 52 0.65
97 24 0.30
98 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (98 bp):
GTATCGATACCATGGTAAGGGTATCAATACAAGTCAACATCGAATCAAAAATGGGAATCGATACC
AGAAAAGAGTATCGATACCATAATATAGTAGTG
Found at i:72287 original size:19 final size:19
Alignment explanation
Indices: 72249--72300 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
72239 AAAAATTGGA
72249 ATCGATACCATAAAAGAGT
1 ATCGATACCATAAAAGAGT
*
72268 ATCGGTACCATAATATAGTAGT
1 ATCGATACCATAA-A-AG-AGT
*
72290 ATCAATACCAT
1 ATCGATACCAT
72301 GATAGGGGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 12 0.44
20 1 0.04
21 2 0.07
22 12 0.44
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.27
Consensus pattern (19 bp):
ATCGATACCATAAAAGAGT
Found at i:72298 original size:22 final size:19
Alignment explanation
Indices: 72253--72300 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
72243 ATTGGAATCG
*
72253 ATACCATAAAAGAGTATCG
1 ATACCATAAAAGAGTATCA
*
72272 GTACCATAATATAGTAGTATCA
1 ATACCATAA-A-AG-AGTATCA
72294 ATACCAT
1 ATACCAT
72301 GATAGGGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 8 0.35
20 1 0.04
21 2 0.09
22 12 0.52
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.27
Consensus pattern (19 bp):
ATACCATAAAAGAGTATCA
Found at i:72720 original size:57 final size:57
Alignment explanation
Indices: 72659--73143 Score: 756
Period size: 57 Copynumber: 8.5 Consensus size: 57
72649 GTGCAAAATA
* *
72659 TAAGAAGTCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTATGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * * *
72716 TAAGAAATCATACTAAGTGTATGAATTTCAGACAGGGCATTACGTGCGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * *
72773 TAACAAATCATACTAAGTGTATAAATTTCAGATAGGGCGTTTCGTACTCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
72830 TAACAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTGCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
72887 TAAGAAATCATACAAAGTGTATGAATTTCAGATAGGGCGTTTTGTACGCTAAAATG-
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* * ** *
72943 TAAGAAATCATACTAAGTGTATGAATTTCATATAGGGCGTTTCATATTCTAAAATGA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
73000 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCATTTCGTACGCTAAAATGT
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
* *
73057 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACCCTAAAATGA
1 TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
*
73114 TAAGGAAATCATACTATGTGTATGAATTTC
1 TAA-GAAATCATACTAAGTGTATGAATTTC
73144 CGTATGGGAA
Statistics
Matches: 390, Mismatches: 36, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
56 50 0.13
57 315 0.81
58 25 0.06
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (57 bp):
TAAGAAATCATACTAAGTGTATGAATTTCAGATAGGGCGTTTCGTACGCTAAAATGT
Found at i:73836 original size:45 final size:45
Alignment explanation
Indices: 73740--73838 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 45
73730 ATAATTGTAT
* * * * * *
73740 GAAAGGATTCCATACATGAAATGTATAATAATGTATCAAAGGAAT
1 GAAAGGATGCCATAAATGAAAGGTATAATAATGAATCAAAAGAAG
*
73785 GAAAGGATGCCATAAATGAAAGGTATAATAGTGAAT-AAAAGATAG
1 GAAAGGATGCCATAAATGAAAGGTATAATAATGAATCAAAAGA-AG
*
73830 GTAAGGATG
1 GAAAGGATG
73839 AAATAATTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
44 5 0.11
45 40 0.89
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.23
Consensus pattern (45 bp):
GAAAGGATGCCATAAATGAAAGGTATAATAATGAATCAAAAGAAG
Found at i:77808 original size:52 final size:52
Alignment explanation
Indices: 77743--77861 Score: 211
Period size: 52 Copynumber: 2.3 Consensus size: 52
77733 AAAAGACTAC
*
77743 CTCTCGATGCTCTTACATTGCCAAGACATGTTTTACCAAAACCCCAGGCGAT
1 CTCTCGATGCTCTTACATTGCCAAGACATGTTTTACCAAAACCCCAGACGAT
* *
77795 CTCTCGATACTCTTACATTGCCAATACATGTTTTACCAAAACCCCAGACGAT
1 CTCTCGATGCTCTTACATTGCCAAGACATGTTTTACCAAAACCCCAGACGAT
77847 CTCTCGATGCTCTTA
1 CTCTCGATGCTCTTA
77862 TAGAGTTAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (52 bp):
CTCTCGATGCTCTTACATTGCCAAGACATGTTTTACCAAAACCCCAGACGAT
Found at i:85085 original size:12 final size:12
Alignment explanation
Indices: 85068--85094 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
85058 TAACTCCAAG
85068 GAATTAGTATTA
1 GAATTAGTATTA
85080 GAATTAGTATTA
1 GAATTAGTATTA
85092 GAA
1 GAA
85095 GAAGAAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (12 bp):
GAATTAGTATTA
Found at i:95112 original size:101 final size:101
Alignment explanation
Indices: 94951--95135 Score: 228
Period size: 101 Copynumber: 1.8 Consensus size: 101
94941 CATCTACAAT
** * * *
94951 TTCTTTGACCTGAATATAGAGATGCCCTCAACACAAAAATCTGTTCAATACCCATTTGACATGAT
1 TTCTTTGACCTGAATATAGAGATGCCCTCAACACAAAAATCAATTCAAAACCCATATGACACGAT
*
95016 GCCTTCAAGTTTCAGGGGATGCATTTAACTGTGAGC
66 GCCTTCAAGTTTAAGGGGATGCATTTAACTGTGAGC
* * * * * *
95052 TTCTTTGACCTTAATATGGAGATG-CCTGCGACACAACACTCAATTCAAAACCCCTATGACACGA
1 TTCTTTGACCTGAATATAGAGATGCCCT-CAACACAAAAATCAATTCAAAACCCATATGACACGA
* *
95116 TGTCTTCCAGTTTAAGGGGA
65 TGCCTTCAAGTTTAAGGGGA
95136 AGGCATTCAA
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
100 3 0.04
101 66 0.96
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (101 bp):
TTCTTTGACCTGAATATAGAGATGCCCTCAACACAAAAATCAATTCAAAACCCATATGACACGAT
GCCTTCAAGTTTAAGGGGATGCATTTAACTGTGAGC
Found at i:97626 original size:18 final size:18
Alignment explanation
Indices: 97599--97641 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
97589 ATGTGCAGTG
*
97599 GGTGAATGATTCAATAAA
1 GGTGATTGATTCAATAAA
97617 GGTGATTGATTCAATAAA
1 GGTGATTGATTCAATAAA
*
97635 GGAGATT
1 GGTGATT
97642 CTTGATCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.30
Consensus pattern (18 bp):
GGTGATTGATTCAATAAA
Found at i:97816 original size:28 final size:28
Alignment explanation
Indices: 97785--97851 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
97775 AAAAAATGTT
*
97785 TTAAATATATGTATGAATTTAAGTTTAG
1 TTAAATATATGTATGAATTTAAGTTTAA
* *
97813 TTAAATATACGTATGAATTTGAGTTTAA
1 TTAAATATATGTATGAATTTAAGTTTAA
97841 TTAAATATATG
1 TTAAATATATG
97852 GTTATTGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.45
Consensus pattern (28 bp):
TTAAATATATGTATGAATTTAAGTTTAA
Found at i:100236 original size:22 final size:22
Alignment explanation
Indices: 100197--100260 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
100187 GACCAGTTTG
*
100197 ACCGTTGATCATTGATCGGTCAA
1 ACCGTTGAT-TTTGATCGGTCAA
* *
100220 ACCGTTGATTTTGATCGATCAG
1 ACCGTTGATTTTGATCGGTCAA
* * *
100242 ACTGTTGACTTTGACCGGT
1 ACCGTTGATTTTGATCGGT
100261 ATGACCGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
22 25 0.74
23 9 0.26
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (22 bp):
ACCGTTGATTTTGATCGGTCAA
Found at i:104791 original size:22 final size:22
Alignment explanation
Indices: 104728--104797 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
104718 ACCCAAATCG
* * *
104728 TTGACCGGTCAGATTGTTGACT
1 TTGATCGGTCTGACTGTTGACT
* **
104750 TTGATCGAT-TAGACCATTGACT
1 TTGATCGGTCT-GACTGTTGACT
104772 TTGATCGGTCTGACTGTTGACT
1 TTGATCGGTCTGACTGTTGACT
104794 TTGA
1 TTGA
104798 CTTTGACCGA
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
22 36 0.97
23 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (22 bp):
TTGATCGGTCTGACTGTTGACT
Found at i:112014 original size:19 final size:18
Alignment explanation
Indices: 111976--112037 Score: 67
Period size: 19 Copynumber: 3.5 Consensus size: 18
111966 TGACCCGTTA
111976 ACTTTGACT-GAACCATTG
1 ACTTTGACTAG-ACCATTG
111994 ACTTTGACTAGACCTATTG
1 ACTTTGACTAGACC-ATTG
* *
112013 ACTTTAACTAGA-GA-TG
1 ACTTTGACTAGACCATTG
112029 ACTTTGACT
1 ACTTTGACT
112038 TTGACCAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
16 10 0.26
17 1 0.03
18 12 0.31
19 16 0.41
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (18 bp):
ACTTTGACTAGACCATTG
Found at i:112051 original size:16 final size:17
Alignment explanation
Indices: 112032--112072 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
112022 AGAGATGACT
* *
112032 TTGACTTTGA-CCAATG
1 TTGACTTTGATCAAAAG
112048 TTGACTTTGATCAAAAG
1 TTGACTTTGATCAAAAG
112065 TTGACTTT
1 TTGACTTT
112073 TTTAAAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (17 bp):
TTGACTTTGATCAAAAG
Found at i:112334 original size:18 final size:18
Alignment explanation
Indices: 112311--112345 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
112301 CGGACTGATC
112311 CGTATGGTTTTGTAAACT
1 CGTATGGTTTTGTAAACT
112329 CGTATGGTTTTGTAAAC
1 CGTATGGTTTTGTAAAC
112346 CTTCATATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (18 bp):
CGTATGGTTTTGTAAACT
Found at i:114977 original size:24 final size:24
Alignment explanation
Indices: 114949--115002 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
114939 TAAACATAGG
* *
114949 ATCCGATTCAACAAAATATTTACA
1 ATCCGAATCAACAAAATATTCACA
*
114973 ATCCGAATCAACTAAATATTCACA
1 ATCCGAATCAACAAAATATTCACA
*
114997 GTCCGA
1 ATCCGA
115003 CTAAATATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.24, G:0.07, T:0.26
Consensus pattern (24 bp):
ATCCGAATCAACAAAATATTCACA
Found at i:115158 original size:3 final size:3
Alignment explanation
Indices: 115144--115209 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
115134 TTTATAAAAA
*
115144 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
115192 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
115210 ACCCTACCCA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:115347 original size:2 final size:2
Alignment explanation
Indices: 115342--115391 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
115332 TTTCTTATTT
115342 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
115384 TA TA TA TA
1 TA TA TA TA
115392 AGTAATAGGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:120281 original size:32 final size:32
Alignment explanation
Indices: 120245--120318 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 32
120235 GCATCTTTAA
*
120245 AGATTCAACAGCAAATGTTGGGGCATAGTTGG
1 AGATTCAACAGCAAATATTGGGGCATAGTTGG
* *** * *
120277 AGATTAAACATTGAATATTGGGGTATATTTGG
1 AGATTCAACAGCAAATATTGGGGCATAGTTGG
*
120309 GGATTCAACA
1 AGATTCAACA
120319 TCCTGATGCA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (32 bp):
AGATTCAACAGCAAATATTGGGGCATAGTTGG
Found at i:120686 original size:64 final size:63
Alignment explanation
Indices: 120580--120708 Score: 195
Period size: 64 Copynumber: 2.0 Consensus size: 63
120570 GGAGCGTCTG
* * *
120580 TCAACAAACAACTTTCCATTTCATTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGCAC
1 TCAACAAACAACTTTCCATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAAC
* * *
120643 TCAACAAATAATTTTCCAGTTTCATTCAGAGTCAATTTTAACTTCACAACGAAGGATATTGAAC
1 TCAACAAACAACTTTCCA-TTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAAC
120707 TC
1 TC
120709 GAAACGACAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
63 16 0.27
64 43 0.73
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (63 bp):
TCAACAAACAACTTTCCATTTCATTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGAAC
Found at i:121005 original size:43 final size:43
Alignment explanation
Indices: 120915--121027 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 43
120905 AGAAGGGGTT
* * * *
120915 ATCCATGATTTCAACTCCATGACGAAGAATATCGTACCTACGG
1 ATCCACGATTTCAACTCCACGACGAAGAATATCGTACCCACGC
* * * * *
120958 ATCCACGATTTTAACTCCACGACGGAGGATATCGTGCCCATGC
1 ATCCACGATTTCAACTCCACGACGAAGAATATCGTACCCACGC
* * *
121001 ATCCACGGTTTCAATTTCACGACGAAG
1 ATCCACGATTTCAACTCCACGACGAAG
121028 GGAATCGTAC
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACGAAGAATATCGTACCCACGC
Found at i:121624 original size:43 final size:43
Alignment explanation
Indices: 121503--121624 Score: 156
Period size: 43 Copynumber: 2.8 Consensus size: 43
121493 CGAAGGGGCT
* * **
121503 ATCCATGATTTTAACTCCACGAC-ATAGGATATCGTACCCACGG
1 ATCCATGATTTCAACTCCACGACGA-AGGATATCGTGCCCACAC
* *
121546 ATCCATGATTTCAACTCCACGACGGAGAATATCGTGCCCACAC
1 ATCCATGATTTCAACTCCACGACGAAGGATATCGTGCCCACAC
* *
121589 ATCCACGATTTCAACTTCACGACGAAGGATATCGTG
1 ATCCATGATTTCAACTCCACGACGAAGGATATCGTG
121625 TTCACCAGCA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
ATCCATGATTTCAACTCCACGACGAAGGATATCGTGCCCACAC
Found at i:121701 original size:207 final size:205
Alignment explanation
Indices: 121439--122036 Score: 822
Period size: 207 Copynumber: 2.9 Consensus size: 205
121429 ATAGCATAAG
* * *
121439 CTTGGATTTCAACTTCACGATGAATGATATTCAAGTCAAGGTTCAACTTCACGACGAAGGGGCTA
1 CTTGGATTTCAACTTCACGACGAAAGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCTA
* ** *
121504 TCCATGATTTTAACTCCACGACATAGGATATCGTACCCACGGATCCATGATTTCAACTCCACGAC
66 TCCACGATTTTAACTCCACGACGGAGGATATCGTACCCACGGATCCACGATTTCAACTCCACGAC
* *
121569 GGAGAATATCGTGCCCACACATCCACGATTTCAACTTCACGACGAAGGATATCGTGTTCA-CCAG
131 GGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACGACGAAGGA-ATCGTGTCCACCCA-
* *
121633 CAGTA-ATGCAACC
194 CA--ACATACAACA
* * * * * *
121646 CTTGGATTTCAATTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACGACGAATGGGCCA
1 CTTGGATTTCAACTTCACGACGAAAGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCTA
*
121711 TCCACGATTTTAACTTCACGACGGAGGATATCGTACCCACGGATCCACGATTTCAACTCCACGAC
66 TCCACGATTTTAACTCCACGACGGAGGATATCGTACCCACGGATCCACGATTTCAACTCCACGAC
* * * *
121776 GGGGGATATCATGCCCACACAACCACGATTTCAACTTCACGACGAAAGGAATTGTGTCCACCCAC
131 GGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACGACG-AAGGAATCGTGTCCACCCAC
*
121841 AACATACAATA
195 AACATACAACA
* * * * *
121852 CTTAGATTTCAACTTCACGACAAAAGATATTCAAGTCAAAGCTCAACTTCACGATGAAGGGGTTA
1 CTTGGATTTCAACTTCACGACGAAAGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCTA
* * *
121917 TCCACGATTTCAACTCCACGACGGAGAATATCGTACCCACGGATCCACGATTTTAACTCCACGAC
66 TCCACGATTTTAACTCCACGACGGAGGATATCGTACCCACGGATCCACGATTTCAACTCCACGAC
* * *
121982 GGAGGATATCGTGCCCACGCATCCACGGTTTCAATTTCACGACGAAGGGAATCGT
131 GGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACGACGAA-GGAATCGT
122037 ACATACAAAC
Statistics
Matches: 343, Mismatches: 44, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
205 3 0.01
206 165 0.48
207 167 0.49
208 8 0.02
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (205 bp):
CTTGGATTTCAACTTCACGACGAAAGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGGGCTA
TCCACGATTTTAACTCCACGACGGAGGATATCGTACCCACGGATCCACGATTTCAACTCCACGAC
GGAGGATATCGTGCCCACACATCCACGATTTCAACTTCACGACGAAGGAATCGTGTCCACCCACA
ACATACAACA
Found at i:121774 original size:43 final size:43
Alignment explanation
Indices: 121709--121819 Score: 150
Period size: 43 Copynumber: 2.6 Consensus size: 43
121699 ACGAATGGGC
* * *
121709 CATCCACGATTTTAACTTCACGACGGAGGATATCGTACCCACG
1 CATCCACGATTTCAACTTCACGACGGAGGATATCATACCCACA
* * * *
121752 GATCCACGATTTCAACTCCACGACGGGGGATATCATGCCCACA
1 CATCCACGATTTCAACTTCACGACGGAGGATATCATACCCACA
*
121795 CAACCACGATTTCAACTTCACGACG
1 CATCCACGATTTCAACTTCACGACG
121820 AAAGGAATTG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (43 bp):
CATCCACGATTTCAACTTCACGACGGAGGATATCATACCCACA
Found at i:121964 original size:43 final size:43
Alignment explanation
Indices: 121916--122025 Score: 157
Period size: 43 Copynumber: 2.6 Consensus size: 43
121906 TGAAGGGGTT
*
121916 ATCCACGATTTCAACTCCACGACGGAGAATATCGTACCCACGG
1 ATCCACGATTTCAACTCCACGACGGAGAATATCGTACCCACGC
* * *
121959 ATCCACGATTTTAACTCCACGACGGAGGATATCGTGCCCACGC
1 ATCCACGATTTCAACTCCACGACGGAGAATATCGTACCCACGC
* * *
122002 ATCCACGGTTTCAATTTCACGACG
1 ATCCACGATTTCAACTCCACGACG
122026 AAGGGAATCG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACGGAGAATATCGTACCCACGC
Found at i:122036 original size:43 final size:43
Alignment explanation
Indices: 121916--122038 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
121906 TGAAGGGGTT
* * *
121916 ATCCACGATTTCAACTCCACGACGGAGAATATCGTACCCACGG
1 ATCCACGATTTCAACTCCACGACGAAGGATATCGTACCCACGC
* * *
121959 ATCCACGATTTTAACTCCACGACGGAGGATATCGTGCCCACGC
1 ATCCACGATTTCAACTCCACGACGAAGGATATCGTACCCACGC
* * *
122002 ATCCACGGTTTCAATTTCACGACGAAGGGA-ATCGTAC
1 ATCCACGATTTCAACTCCACGACGAA-GGATATCGTAC
122039 ATACAAACGG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
43 66 0.96
44 3 0.04
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACGAAGGATATCGTACCCACGC
Found at i:122557 original size:43 final size:43
Alignment explanation
Indices: 122504--122624 Score: 152
Period size: 43 Copynumber: 2.8 Consensus size: 43
122494 CGAAGGGGCT
* *
122504 ATCCACGATTTCAACTCCACGACGAAGGATATCGTACCCACAG
1 ATCCACGATTTCAACTCCACGACGAAGGATATCATACCCACAC
* * * * *
122547 ATCCATGATTTCAACTCCACGACGGAGTATATCATGCCCATAC
1 ATCCACGATTTCAACTCCACGACGAAGGATATCATACCCACAC
* * *
122590 ATCCACGTTTTCAACTTCACGACGAATGATATCAT
1 ATCCACGATTTCAACTCCACGACGAAGGATATCAT
122625 GTTCACCAGT
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.25
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACGACGAAGGATATCATACCCACAC
Found at i:123049 original size:36 final size:37
Alignment explanation
Indices: 122929--123089 Score: 157
Period size: 37 Copynumber: 4.4 Consensus size: 37
122919 CGTTGAATAT
* *
122929 GTTTCCCTTGAAACAAAG-TTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
* * * * * *
122965 ATTTCTTTTGGAACCAGGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
* * *
123002 -TATTATATTGAAA-GAAGTTTTGTCTCCCTTGAGACA
1 GT-TTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
* * * *
123038 GTTTCCCTTGAAACAAAATTTTGTTTCCCTTGAGACG
1 GTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
123075 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
123090 TAAAATCTTT
Statistics
Matches: 101, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
36 41 0.41
37 60 0.59
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (37 bp):
GTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACA
Found at i:123147 original size:67 final size:66
Alignment explanation
Indices: 123030--123193 Score: 172
Period size: 67 Copynumber: 2.5 Consensus size: 66
123020 TTTGTCTCCC
* * * * * * *
123030 TTGAGA-CAGTTTCCCTTGAAACAAAATTTTGTTTCCCTTGAGACGGTTTCTCT-TGAAACATAA
1 TTGAGATCA-TTTCCCTTGAAAC-AAGTTTTATCTCTCTAGAGACAGTTTCT-TGTGAAACACAA
123093 AATCT
63 AA-CT
* *
123098 TTGA-ATCATTTCCCTTTGAAACGAGTTTTATCTCTCTAGAGACAGTTTCTTGTGAAACACCAAA
1 TTGAGATCATTTCCC-TTGAAACAAGTTTTATCTCTCTAGAGACAGTTTCTTGTGAAACACAAAA
123162 CT
65 CT
*
123164 TTGAGATTATTTCCCTTGAAACAAGTTTTA
1 TTGAGATCATTTCCCTTGAAACAAGTTTTA
123194 GTTTCCTTGA
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
66 21 0.26
67 47 0.58
68 13 0.16
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (66 bp):
TTGAGATCATTTCCCTTGAAACAAGTTTTATCTCTCTAGAGACAGTTTCTTGTGAAACACAAAAC
T
Found at i:123291 original size:69 final size:68
Alignment explanation
Indices: 123209--123368 Score: 205
Period size: 69 Copynumber: 2.3 Consensus size: 68
123199 CTTGAGATCA
* * *
123209 TTTGAGATGTTTCTCTTGAAACAAATCCCATT-TTCTTTAAGATCTTTTCTCATGAAACAATAAC
1 TTTGAGATGTTTCTCTTGAAACAAATCCCATTATT-TTTAAGATCGTTTCTCATGAAACAACAAA
123273 TAAAC
65 T-AAC
* * * *
123278 TTTGAGATATTTCTCTTGAGACAAATCCTATTATTTTTTAGATCGTTTCTCATGAAACAACAAAT
1 TTTGAGATGTTTCTCTTGAAACAAATCCCATTATTTTTAAGATCGTTTCTCATGAAACAACAAAT
*
123343 ATC
66 AAC
*
123346 TTTGAGATCGTTTCCCTTGAAAC
1 TTTGAGAT-GTTTCTCTTGAAAC
123369 GAATTTTGTC
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
68 10 0.13
69 66 0.85
70 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (68 bp):
TTTGAGATGTTTCTCTTGAAACAAATCCCATTATTTTTAAGATCGTTTCTCATGAAACAACAAAT
AAC
Found at i:123564 original size:43 final size:43
Alignment explanation
Indices: 123459--123874 Score: 158
Period size: 43 Copynumber: 9.6 Consensus size: 43
123449 TAGTCTGTCA
* * *
123459 TCCTCATCACGTAGGAACCGTGTC-ATCCCT---CGACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCAAT-CTTAGATGACCAG-CCG
** *
123499 TCCTCATCACGTAGGAGTCGTGTCAATCTTAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCAATCTTAGATGACCAGCCG
* * * * * **
123542 TCCTCATCACGTAAGAACCGTGTTATTATCCCTAATGATGGCCTGTAG
1 TCCTCATCACGTAGGAACCGTGTCA--AT--CTTA-GATGACCAGCCG
* * * *
123590 TCCTCATCAAGTAGGAACCGTGTC-ATCCCTCGAT---CAGATC-
1 TCCTCATCACGTAGGAACCGTGTCAAT-CTTAGATGACCAG-CCG
* * * * * *
123630 TCCTCATCACGTAAGAACCGTGTTAACCTTAGATAACTAGCCT
1 TCCTCATCACGTAGGAACCGTGTCAATCTTAGATGACCAGCCG
* * * * * *
123673 TTCTCATCACGTAGGAATCGTGTTATTATCCCTAATGATGGCCTGCCG
1 TCCTCATCACGTAGGAACCGTGTCA--AT--CTTA-GATGACCAGCCG
* *** * *
123721 TCCTCATTACGTAGGAACCGTGTC-ATC--ACCCGACCTGATC-
1 TCCTCATCACGTAGGAACCGTGTCAATCTTAGATGACCAG-CCG
* * * * *
123761 TCCTCATCACGTATGAGCCGTGTCAACCTCAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCAATCTTAGATGACCAGCCG
* ** * *
123804 TACTCATCACGTAGGAACCGTGTTATCACCCTTAGATGACCTGTCG
1 TCCTCATCACGTAGGAACCGTG---TCAATCTTAGATGACCAGCCG
*
123850 TCCTCATCACATAGGAACCGTGTCA
1 TCCTCATCACGTAGGAACCGTGTCA
123875 TCACCTGACC
Statistics
Matches: 276, Mismatches: 71, Indels: 55
0.69 0.18 0.14
Matches are distributed among these distances:
40 78 0.28
41 8 0.03
42 3 0.01
43 81 0.29
44 2 0.01
45 7 0.03
46 36 0.13
47 6 0.02
48 55 0.20
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACCGTGTCAATCTTAGATGACCAGCCG
Found at i:123597 original size:48 final size:48
Alignment explanation
Indices: 123541--123743 Score: 141
Period size: 48 Copynumber: 4.5 Consensus size: 48
123531 ATAACCAGCC
*
123541 GTCCTCATCACGTAAGAACCGTGTTATTATCCCTAATGATGGCCTGTA
1 GTCCTCATCACGTAGGAACCGTGTTATTATCCCTAATGATGGCCTGTA
* * * *
123589 GTCCTCATCAAGTAGGAACCGTG---TCATCCCT--CGAT---CAG-A
1 GTCCTCATCACGTAGGAACCGTGTTATTATCCCTAATGATGGCCTGTA
* * * * *
123628 TCTCCTCATCACGTAAGAACCGTGTTA--A-CCTTAGATAACTAGCCT-T-
1 -GTCCTCATCACGTAGGAACCGTGTTATTATCCCTA-ATGA-TGGCCTGTA
* **
123674 -T-CTCATCACGTAGGAATCGTGTTATTATCCCTAATGATGGCCTGCC
1 GTCCTCATCACGTAGGAACCGTGTTATTATCCCTAATGATGGCCTGTA
*
123720 GTCCTCATTACGTAGGAACCGTGT
1 GTCCTCATCACGTAGGAACCGTGT
123744 CATCACCCGA
Statistics
Matches: 116, Mismatches: 20, Indels: 38
0.67 0.11 0.22
Matches are distributed among these distances:
39 1 0.01
40 25 0.22
41 1 0.01
43 25 0.22
44 7 0.06
45 11 0.09
46 4 0.03
47 2 0.02
48 40 0.34
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (48 bp):
GTCCTCATCACGTAGGAACCGTGTTATTATCCCTAATGATGGCCTGTA
Found at i:123679 original size:131 final size:131
Alignment explanation
Indices: 123435--123923 Score: 585
Period size: 131 Copynumber: 3.7 Consensus size: 131
123425 TCTTGAAACC
* * * *
123435 ATTATCCCTAAAGATAGTCTGTCA-TCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATC
1 ATTATCCCTAATGATGGCCTGT-AGTCCTCATCAAGTAGGAACCGTGTCATCCCTCGACCAGATC
* * * * *
123499 TCCTCATCACGTAGGAGTCGTGTCAATCTTAGATAACCAGCCGTCCTCATCACGTAAGAACCGTG
65 TCCTCATCACGTAAGAGCCGTGTCAACCTTAGATAACCAGCCGTACTCATCACGTAGGAACCGTG
123564 TT
130 TT
*
123566 ATTATCCCTAATGATGGCCTGTAGTCCTCATCAAGTAGGAACCGTGTCATCCCTCGATCAGATCT
1 ATTATCCCTAATGATGGCCTGTAGTCCTCATCAAGTAGGAACCGTGTCATCCCTCGACCAGATCT
* * * * * *
123631 CCTCATCACGTAAGAACCGTGTTAACCTTAGATAACTAGCCTTTCTCATCACGTAGGAATCGTGT
66 CCTCATCACGTAAGAGCCGTGTCAACCTTAGATAACCAGCCGTACTCATCACGTAGGAACCGTGT
123696 T
131 T
** * * *
123697 ATTATCCCTAATGATGGCCTGCCGTCCTCATTACGTAGGAACCGTGTCATCACC-CGACCTGATC
1 ATTATCCCTAATGATGGCCTGTAGTCCTCATCAAGTAGGAACCGTGTCATC-CCTCGACCAGATC
* *
123761 TCCTCATCACGTATGAGCCGTGTCAACCTCAGATAACCAGCCGTACTCATCACGTAGGAACCGTG
65 TCCTCATCACGTAAGAGCCGTGTCAACCTTAGATAACCAGCCGTACTCATCACGTAGGAACCGTG
123826 TT
130 TT
* * * * * **
123828 ATCA-CCCTTA-GATGACCTGTCGTCCTCATCACA-TAGGAACCGTGTCATCACCT-GACCTGGC
1 ATTATCCCTAATGATGGCCTGTAGTCCTCATCA-AGTAGGAACCGTGTCATC-CCTCGACCAGAT
* * * *
123889 CTCCTTATCACGTAGGAGTCATGTCAAGCCTTAGA
64 CTCCTCATCACGTAAGAGCCGTGTCAA-CCTTAGA
123924 CGACCAGAAC
Statistics
Matches: 311, Mismatches: 42, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
129 66 0.21
130 12 0.04
131 231 0.74
132 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (131 bp):
ATTATCCCTAATGATGGCCTGTAGTCCTCATCAAGTAGGAACCGTGTCATCCCTCGACCAGATCT
CCTCATCACGTAAGAGCCGTGTCAACCTTAGATAACCAGCCGTACTCATCACGTAGGAACCGTGT
T
Found at i:123878 original size:46 final size:45
Alignment explanation
Indices: 123459--123879 Score: 208
Period size: 40 Copynumber: 9.7 Consensus size: 45
123449 TAGTCTGTCA
* * *
123459 TCCTCATCACGTAGGAACCGTGTCAT--CCCT---CGACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCTG-CCG
** * * * *
123499 TCCTCATCACGTAGGAGTCGTGTCA--ATCTTAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCTGCCG
* * * * **
123542 TCCTCATCACGTAAGAACCGTGTTATTATCCCTAATGATGGCCTGTAG
1 TCCTCATCACGTAGGAACCGTGTCATCA-CCCT-A-GATGACCTGCCG
* * * **
123590 TCCTCATCAAGTAGGAACCGTGTCAT--CCCTCGATCAGAT--C-
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCTGCCG
* * * * *
123630 TCCTCATCACGTAAGAACCGTGT--TAACCTTAGAT-AACTAGCCT
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCT-GCCG
* * * * *
123673 TTCTCATCACGTAGGAATCGTGTTATTATCCCTAATGATGGCCTGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCA-CCCT-A-GATGACCTGCCG
* *
123721 TCCTCATTACGTAGGAACCGTGTCATCACCC-----GACCTGATC-
1 TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCTG-CCG
* * * *
123761 TCCTCATCACGTATGAGCCGTGTCA--A-CCTCAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCATCACCCT-AGATGACCTGCCG
* * *
123804 TACTCATCACGTAGGAACCGTGTTATCACCCTTAGATGACCTGTCG
1 TCCTCATCACGTAGGAACCGTGTCATCACCC-TAGATGACCTGCCG
*
123850 TCCTCATCACATAGGAACCGTGTCATCACC
1 TCCTCATCACGTAGGAACCGTGTCATCACC
123880 TGACCTGGCC
Statistics
Matches: 283, Mismatches: 64, Indels: 62
0.69 0.16 0.15
Matches are distributed among these distances:
37 2 0.01
38 2 0.01
39 2 0.01
40 79 0.28
41 1 0.00
42 3 0.01
43 75 0.27
45 8 0.03
46 44 0.16
47 6 0.02
48 59 0.21
49 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.27
Consensus pattern (45 bp):
TCCTCATCACGTAGGAACCGTGTCATCACCCTAGATGACCTGCCG
Found at i:124094 original size:3 final size:3
Alignment explanation
Indices: 124086--124134 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
124076 GTTTTAAAAA
*
124086 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
124134 A
1 A
124135 CCCTACCCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:124631 original size:152 final size:147
Alignment explanation
Indices: 124418--124785 Score: 413
Period size: 146 Copynumber: 2.5 Consensus size: 147
124408 GACCTCCGAT
*
124418 CAACATTCCAAACGGTCAAAAGTTGCGCGATGTCAACACGAACAACATACT-AAAAATTCAAGAC
1 CAACATTCCGAACGGTCAAAAGTTGCGCGATGTCAACACGAACAACATACTGAAAAA-TCAAGAC
* * *
124482 GATCGGACGGTGGACGGTGGACGGTGGCGGATCGGATAAAACCAAA-CTAGAAGGTTTTTGGCCT
65 GAT----C--TGGAAGGTGGACGGTGGCGGATCGGAGAAAA-CAAATCCAGAAGGTTTTTGGCCT
*
124546 -TTGGCCGGCAATAGAGA-CCACGAA
123 CTT-GCCGACAATAGAGATCCACGAA
* *
124570 CAACATACCGAACGGTCAAAAGTTGTGCGATGTCAACACGAACAACATACTGAAAAATCAAGACG
1 CAACATTCCGAACGGTCAAAAGTTGCGCGATGTCAACACGAACAACATACTGAAAAATCAAGACG
* * * * * *
124635 AT-TTGAAGGTGGGCGGTGGCGGATTGTAGAAAACAAATCCGGACGGTTTTTGGCCTCTTGCCGA
66 ATCTGGAAGGTGGACGGTGGCGGATCGGAGAAAACAAATCCAGAAGGTTTTTGGCCTCTTGCCGA
* * ** *
124699 CGATCGAGATCTTCGAT
131 CAATAGAGATCCACGAA
* * * * *
124716 CAACATTCCGAACGGTGAAAAGTTACGAGATGTCAACACGAACAACATATTGAAAAATCATGACG
1 CAACATTCCGAACGGTCAAAAGTTGCGCGATGTCAACACGAACAACATACTGAAAAATCAAGACG
124781 ATCTG
66 ATCTG
124786 ATAGTGGATG
Statistics
Matches: 185, Mismatches: 26, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
144 4 0.02
145 51 0.28
146 66 0.36
147 1 0.01
152 58 0.31
153 5 0.03
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (147 bp):
CAACATTCCGAACGGTCAAAAGTTGCGCGATGTCAACACGAACAACATACTGAAAAATCAAGACG
ATCTGGAAGGTGGACGGTGGCGGATCGGAGAAAACAAATCCAGAAGGTTTTTGGCCTCTTGCCGA
CAATAGAGATCCACGAA
Done.