Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004129.1 Hibiscus syriacus cultivar Beakdansim tig00009035_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: 91762
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1647 original size:23 final size:22
Alignment explanation
Indices: 1620--1684 Score: 89
Period size: 20 Copynumber: 3.0 Consensus size: 22
1610 GCGGACGACA
1620 GACGGCGGCCGGCGATGATAAAC
1 GACGGCGG-CGGCGATGATAAAC
1643 GACGGC-G-GGCGATGATAAAC
1 GACGGCGGCGGCGATGATAAAC
*
1663 GACGGCGGGCGGCGATGGTAAA
1 GACGGC-GGCGGCGATGATAAA
1685 GATGAGCTGA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
20 19 0.50
22 2 0.05
23 17 0.45
ACGTcount: A:0.26, C:0.22, G:0.43, T:0.09
Consensus pattern (22 bp):
GACGGCGGCGGCGATGATAAAC
Found at i:3058 original size:2 final size:2
Alignment explanation
Indices: 3051--3083 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3041 AAACACAGTT
3051 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3084 GCAAGATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8089 original size:6 final size:6
Alignment explanation
Indices: 8056--8088 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
8046 TCGGTGCATG
8056 TTTTT- TTTTTC TTTTTC TTTTTC TTTTT- TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
8089 TATCTCGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (6 bp):
TTTTTC
Found at i:8089 original size:12 final size:12
Alignment explanation
Indices: 8056--8089 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
8046 TCGGTGCATG
8056 TTTTTTTTTTCT
1 TTTTTTTTTTCT
*
8068 TTTTCTTTTTCT
1 TTTTTTTTTTCT
8080 TTTTTTTTTT
1 TTTTTTTTTT
8090 ATCTCGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:9152 original size:12 final size:12
Alignment explanation
Indices: 9131--9167 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
9121 AATCAGACAG
*
9131 TGATGTAGATGA
1 TGATGAAGATGA
9143 TGATGAAGATGA
1 TGATGAAGATGA
*
9155 TAATGAAGATGA
1 TGATGAAGATGA
9167 T
1 T
9168 TTAATGGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (12 bp):
TGATGAAGATGA
Found at i:10932 original size:7 final size:7
Alignment explanation
Indices: 10920--10970 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
10910 TGATTTTGTG
10920 AACCTTA
1 AACCTTA
10927 AACCTTA
1 AACCTTA
*
10934 AACCCTA
1 AACCTTA
*
10941 AACCCTA
1 AACCTTA
*
10948 AACTTTA
1 AACCTTA
*
10955 AACCCTA
1 AACCTTA
*
10962 AATCTTA
1 AACCTTA
10969 AA
1 AA
10971 AATATTTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (7 bp):
AACCTTA
Found at i:10942 original size:14 final size:14
Alignment explanation
Indices: 10920--10970 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
10910 TGATTTTGTG
*
10920 AACCTTAAACCTTA
1 AACCTTAAACCCTA
*
10934 AACCCTAAACCCTA
1 AACCTTAAACCCTA
*
10948 AACTTTAAACCCTA
1 AACCTTAAACCCTA
*
10962 AATCTTAAA
1 AACCTTAAA
10971 AATATTTTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (14 bp):
AACCTTAAACCCTA
Found at i:10970 original size:21 final size:21
Alignment explanation
Indices: 10920--10970 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
10910 TGATTTTGTG
10920 AACCTTAAACCTTAAACCCTA
1 AACCTTAAACCTTAAACCCTA
* *
10941 AACCCTAAACTTTAAACCCTA
1 AACCTTAAACCTTAAACCCTA
*
10962 AATCTTAAA
1 AACCTTAAA
10971 AATATTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (21 bp):
AACCTTAAACCTTAAACCCTA
Found at i:11287 original size:14 final size:14
Alignment explanation
Indices: 11265--11308 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
11255 TTATTGTTGA
* *
11265 AAACTCTAAATGCT
1 AAACACTAAATCCT
* *
11279 AAACCCTAAACCCT
1 AAACACTAAATCCT
11293 AAACACTAAATCCT
1 AAACACTAAATCCT
11307 AA
1 AA
11309 CCATTCTCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (14 bp):
AAACACTAAATCCT
Found at i:11507 original size:288 final size:290
Alignment explanation
Indices: 10990--11704 Score: 1139
Period size: 288 Copynumber: 2.5 Consensus size: 290
10980 GTTATTGCTA
* *
10990 AAAACCCTAAACCTTAAACACTAAACCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAA
1 AAAACCCTAAACCCTAAACACTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAA
11055 AACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACA
66 AACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACA
* * *
11120 TATCATGAATTTATAAAGATTTTCAGCAATAATCAAAATATTTTAGGGTTTAAGGTTCCAAAATC
131 TATCATGAACTTATAAAGATTTTCAGCAATAACCAAAATATTTTAGGGTTTAAGCTTCCAAAATC
11185 AATATACAACAAATAATATAAGGAACTATTGA-TTTG-TAAACCTTAAACCCTAAACCCTAAAAT
196 AATATACAACAAATAATATAAGGAACTATTGATTTTGCTAAACCTTAAACCCTAAACCCTAAAAT
* * **
11248 ATTTTGGTTATTGTTGAAAACTCTAAATGC
261 ATTTTGGTTATTATTGAAAACCCTAAAACC
*
11278 TAAACCCTAAACCCTAAACACTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAA
1 AAAACCCTAAACCCTAAACACTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAA
*
11343 ACCAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACA
66 AACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACA
*
11408 TATCATGAACTTATAAAGGTTTTCAGCAATAACCAAAATATTTTAGGGTTTAAGCTTCCAAAATC
131 TATCATGAACTTATAAAGATTTTCAGCAATAACCAAAATATTTTAGGGTTTAAGCTTCCAAAATC
* * * *
11473 AATATACAACAAATAATATCAGTAACTATTGATTTTGCAAACCCTAAATCTTAAACCTTAAACCC
196 AATATACAACAAATAATATAAGGAACTATTGATTTTG------CTAAACCTTAAACCCTAAACCC
* *
11538 TAAAATTTTTTGGTTGTTATTGAAAACCCTAAAACC
255 TAAAATATTTTGGTTATTATTGAAAACCCTAAAACC
** *
11574 AAAAATCTAAACCCTAAACACTAAAT-CTAAACATTCTCCCTCCAATCAATTTCTTCTTATAAAA
1 AAAACCCTAAACCCTAAACACTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAA
* * *
11638 AATAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCTTTCATTACCCTCAACA
66 AACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACA
11703 TA
131 TA
11705 CCATTGCCCT
Statistics
Matches: 393, Mismatches: 26, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
288 217 0.55
289 4 0.01
295 100 0.25
296 72 0.18
ACGTcount: A:0.39, C:0.25, G:0.06, T:0.30
Consensus pattern (290 bp):
AAAACCCTAAACCCTAAACACTAAATCCTAACCATTCTCCCTCCAATCAATTTCTTCTTATAAAA
AACAAATATGTAACCACCATCATGGTAGATATCACCATCCTCTACCCCCTTCATTGCCCTCAACA
TATCATGAACTTATAAAGATTTTCAGCAATAACCAAAATATTTTAGGGTTTAAGCTTCCAAAATC
AATATACAACAAATAATATAAGGAACTATTGATTTTGCTAAACCTTAAACCCTAAACCCTAAAAT
ATTTTGGTTATTATTGAAAACCCTAAAACC
Found at i:11910 original size:22 final size:21
Alignment explanation
Indices: 11888--11928 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
11878 CTATTTTTTA
11888 AATCA-TTAGATAATAAAAATT
1 AATCATTTA-ATAATAAAAATT
11909 AATCATTTAATAATAAAAAT
1 AATCATTTAATAATAAAAAT
11929 AATATTATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
AATCATTTAATAATAAAAATT
Found at i:11912 original size:21 final size:19
Alignment explanation
Indices: 11888--11940 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
11878 CTATTTTTTA
11888 AATCATTAGATAATAAAAATT
1 AATCATTA-ATAATAAAAA-T
11909 AATCATTTAATAATAAAAAT
1 AATCA-TTAATAATAAAAAT
11929 AAT-ATTATATAA
1 AATCATTA-ATAA
11941 AACAAATCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 5 0.17
20 4 0.13
21 15 0.50
22 3 0.10
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (19 bp):
AATCATTAATAATAAAAAT
Found at i:12552 original size:30 final size:30
Alignment explanation
Indices: 12506--12582 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
12496 TATTTGAAAA
*
12506 GTTA-AAAATCGGTCACTAATGTTATCCTTT
1 GTTACAAAAT-GGTCACTAACGTTATCCTTT
*
12536 GTTACAAAATGGTCACTAACGTTATCGTTT
1 GTTACAAAATGGTCACTAACGTTATCCTTT
*
12566 GTTACAAAATGATCACT
1 GTTACAAAATGGTCACT
12583 CATCGTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 38 0.88
31 5 0.12
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.36
Consensus pattern (30 bp):
GTTACAAAATGGTCACTAACGTTATCCTTT
Found at i:13997 original size:18 final size:18
Alignment explanation
Indices: 13974--14008 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
13964 ATTAAAAATA
13974 ATTAAA-TTAGGTATAAAG
1 ATTAAATTTAGG-ATAAAG
13992 ATTAAATTTAGGATAAA
1 ATTAAATTTAGGATAAA
14009 TTACGCGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (18 bp):
ATTAAATTTAGGATAAAG
Found at i:25938 original size:6 final size:6
Alignment explanation
Indices: 25927--25959 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
25917 ACTCTAAAGT
25927 ACATGA ACATGA ACATGA ACATGA ACATGA ACA
1 ACATGA ACATGA ACATGA ACATGA ACATGA ACA
25960 ACATCAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (6 bp):
ACATGA
Found at i:30627 original size:24 final size:24
Alignment explanation
Indices: 30600--30645 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
30590 TATGGTTGGA
30600 GAAGAAGAGAGAAGAGGAAGCATC
1 GAAGAAGAGAGAAGAGGAAGCATC
*
30624 GAAGAAGAGAGACGAGGAAGCA
1 GAAGAAGAGAGAAGAGGAAGCA
30646 GGAGCAATTG
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:0.50, C:0.09, G:0.39, T:0.02
Consensus pattern (24 bp):
GAAGAAGAGAGAAGAGGAAGCATC
Found at i:35489 original size:24 final size:24
Alignment explanation
Indices: 35457--35502 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
35447 TATGGTTGGA
35457 GAAGAAGAGAGAAGAGGAAGCATC
1 GAAGAAGAGAGAAGAGGAAGCATC
*
35481 GAAGAAGAGAGACGAGGAAGCA
1 GAAGAAGAGAGAAGAGGAAGCA
35503 GGAGCAATTG
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:0.50, C:0.09, G:0.39, T:0.02
Consensus pattern (24 bp):
GAAGAAGAGAGAAGAGGAAGCATC
Found at i:40690 original size:24 final size:24
Alignment explanation
Indices: 40638--40691 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
40628 ATGATGATGC
*
40638 AGGGCTTGGGTTGTAAGAAGCACA
1 AGGGCTTGGGTTGTAAGAAGAACA
*
40662 AGGGCTT-GGTTGGTAAGACGAACA
1 AGGGCTTGGGTT-GTAAGAAGAACA
*
40686 GGGGCT
1 AGGGCT
40692 CAACGTTGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.26, C:0.13, G:0.41, T:0.20
Consensus pattern (24 bp):
AGGGCTTGGGTTGTAAGAAGAACA
Found at i:44594 original size:15 final size:16
Alignment explanation
Indices: 44571--44608 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
44561 ACCCGACCCT
*
44571 ATACAATCGGG-TTGG
1 ATACCATCGGGTTTGG
44586 ATACCATCGGGTTTGG
1 ATACCATCGGGTTTGG
*
44602 ATCCCAT
1 ATACCAT
44609 GCCATTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (16 bp):
ATACCATCGGGTTTGG
Found at i:45556 original size:22 final size:22
Alignment explanation
Indices: 45528--45575 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
45518 TTTGAAATAA
45528 TAATAATGATAATAATAAGGGT
1 TAATAATGATAATAATAAGGGT
*
45550 TAATAATGATACTAATAAGGGT
1 TAATAATGATAATAATAAGGGT
45572 TAAT
1 TAAT
45576 TGACTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (22 bp):
TAATAATGATAATAATAAGGGT
Found at i:46072 original size:2 final size:2
Alignment explanation
Indices: 46065--46095 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46055 TGTTTGCAGA
46065 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 A
46096 ACTTTACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46736 original size:21 final size:21
Alignment explanation
Indices: 46692--46736 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
46682 TAATTATGCA
*
46692 TTTAATACCTAAATTATCAGT
1 TTTAATACCTAAATTATCAAT
* * *
46713 TTTAATATCTAATTTTTCAAT
1 TTTAATACCTAAATTATCAAT
46734 TTT
1 TTT
46737 TTTAAAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTAATACCTAAATTATCAAT
Found at i:52917 original size:13 final size:13
Alignment explanation
Indices: 52901--52984 Score: 57
Period size: 13 Copynumber: 6.2 Consensus size: 13
52891 ATGTATAAAT
52901 TAAATTAATATAA
1 TAAATTAATATAA
*
52914 TAAATAAATATAA
1 TAAATTAATATAA
*
52927 TAAAAATAATAATTAA
1 T-AAATTAAT-A-TAA
*
52943 TAATATTAAT-TAT
1 TAA-ATTAATATAA
52956 TAAATATAATAATAA
1 TAAAT-TAAT-ATAA
*
52971 TTAA--AATATAA
1 TAAATTAATATAA
52982 TAA
1 TAA
52985 TATATAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
11 6 0.11
12 5 0.09
13 22 0.39
14 6 0.11
15 8 0.14
16 9 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TAAATTAATATAA
Found at i:52921 original size:22 final size:24
Alignment explanation
Indices: 52895--52994 Score: 75
Period size: 25 Copynumber: 4.1 Consensus size: 24
52885 TTTGAAATGT
52895 ATAAATTAA-ATTAAT-ATAATAA
1 ATAAATTAATATTAATAATAATAA
** *
52917 ATAAATATAATAAAAATAATAATTA
1 ATAAAT-TAATATTAATAATAATAA
52942 ATAATATTAATTATTAA-ATATAAT-A
1 ATAA-ATTAA-TATTAATA-ATAATAA
*
52967 AT-AATTAAAATATAATAATATATAA
1 ATAAATTAATAT-TAATAATA-ATAA
52992 ATA
1 ATA
52995 TAGTAATTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
22 8 0.13
23 14 0.23
24 8 0.13
25 20 0.33
26 11 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAATTAATATTAATAATAATAA
Found at i:52943 original size:16 final size:16
Alignment explanation
Indices: 52924--53004 Score: 55
Period size: 16 Copynumber: 5.2 Consensus size: 16
52914 TAAATAAATA
52924 TAATAAAAATAATAAT
1 TAATAAAAATAATAAT
*
52940 TAAT---AATATTAAT
1 TAATAAAAATAATAAT
* *
52953 TATTAAATATAATAA-
1 TAATAAAAATAATAAT
52968 TAATTAAAATATAATAA-
1 TAA-TAAAA-ATAATAAT
* *
52985 TATATAAATATAGTAAT
1 TA-ATAAAAATAATAAT
53002 TAA
1 TAA
53005 AATAGATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
13 11 0.22
15 2 0.04
16 21 0.42
17 15 0.30
18 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (16 bp):
TAATAAAAATAATAAT
Found at i:53004 original size:46 final size:42
Alignment explanation
Indices: 52929--53036 Score: 71
Period size: 46 Copynumber: 2.5 Consensus size: 42
52919 AAATATAATA
*
52929 AAAATAATAATTAATAATATTAATTATTAAATATAATAATAATTA
1 AAAATAATAATTAATAATATTAATAATTAAATA-AAT-ATAA-TA
* * **
52974 AAATATAATAA-TATATAA-ATATAGTAATTAAAATAGATATTCTA
1 AAA-ATAATAATTA-ATAATAT-TAATAATT-AAATAAATATAATA
53018 TAAAA-AATAATT-ATAATAT
1 -AAAATAATAATTAATAATAT
53037 ATTTTGTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
42 4 0.08
43 7 0.14
44 4 0.08
45 12 0.24
46 19 0.37
47 5 0.10
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (42 bp):
AAAATAATAATTAATAATATTAATAATTAAATAAATATAATA
Found at i:53427 original size:4 final size:4
Alignment explanation
Indices: 53418--53447 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
53408 ATATTTTTTC
53418 TATT TATT TATT TATT TAGTT TATT TATT T
1 TATT TATT TATT TATT TA-TT TATT TATT T
53448 TGGTATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:59818 original size:33 final size:32
Alignment explanation
Indices: 59748--59827 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
59738 GAGTAGACTC
* *
59748 TAATAATAAATATTATAAAAAAACTAAGCCTA
1 TAATAATAAATATTAGAAAAAAACTAACCCTA
59780 TAATAATAAATATTAGGGAAAAAAA-TAAACCCTA
1 TAATAATAAATATTA--GAAAAAAACT-AACCCTA
*
59814 -AATAATAAGTATTA
1 TAATAATAAATATTA
59828 AACATAATTG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 15 0.36
33 14 0.33
34 13 0.31
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (32 bp):
TAATAATAAATATTAGAAAAAAACTAACCCTA
Found at i:62127 original size:12 final size:12
Alignment explanation
Indices: 62110--62143 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
62100 GAAAATAAAG
62110 AAAACTTAATGT
1 AAAACTTAATGT
*
62122 AAAACTTGATGT
1 AAAACTTAATGT
62134 AAAAC-TAATG
1 AAAACTTAATG
62144 GCCCTAGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.50, C:0.09, G:0.12, T:0.29
Consensus pattern (12 bp):
AAAACTTAATGT
Found at i:65524 original size:14 final size:14
Alignment explanation
Indices: 65505--65531 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
65495 ACATACTGAA
65505 TTCAAGGGCTACAG
1 TTCAAGGGCTACAG
65519 TTCAAGGGCTACA
1 TTCAAGGGCTACA
65532 TTATTGTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (14 bp):
TTCAAGGGCTACAG
Found at i:65602 original size:100 final size:100
Alignment explanation
Indices: 65429--65620 Score: 357
Period size: 100 Copynumber: 1.9 Consensus size: 100
65419 AAACATCTAA
*
65429 ACATTATTGTAATTAAAATTGCAGATAAACCATTGCAGGCAACAACATAAGAGTACAATAAACCA
1 ACATTATTGTAATTAAAATTGAAGATAAACCATTGCAGGCAACAACATAAGAGTACAATAAACCA
65494 CACATACTGAATTCAAGGGCTACAGTTCAAGGGCT
66 CACATACTGAATTCAAGGGCTACAGTTCAAGGGCT
**
65529 ACATTATTGTAATTAAAATTGAAGATAAACCATTGCAGGCAACAACATAAGAGTATGATAAACCA
1 ACATTATTGTAATTAAAATTGAAGATAAACCATTGCAGGCAACAACATAAGAGTACAATAAACCA
65594 CACATACTGAATTCAAGGGCTACAGTT
66 CACATACTGAATTCAAGGGCTACAGTT
65621 TAGTGACAAA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (100 bp):
ACATTATTGTAATTAAAATTGAAGATAAACCATTGCAGGCAACAACATAAGAGTACAATAAACCA
CACATACTGAATTCAAGGGCTACAGTTCAAGGGCT
Found at i:66378 original size:24 final size:24
Alignment explanation
Indices: 66351--66398 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
66341 CTGCTAGTTC
66351 AATCCCCGAGTATCGTATTGATAG
1 AATCCCCGAGTATCGTATTGATAG
66375 AATCCCCGAGTATCGTATTGATAG
1 AATCCCCGAGTATCGTATTGATAG
66399 GAGTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (24 bp):
AATCCCCGAGTATCGTATTGATAG
Found at i:70883 original size:29 final size:29
Alignment explanation
Indices: 70848--70929 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
70838 AAACTAAATT
*
70848 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
70877 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
70906 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
70930 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:75681 original size:28 final size:29
Alignment explanation
Indices: 75611--75692 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
75601 CAAACTAAAT
*
75611 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
*
75640 AGATGTCATTGCTTACATCATTTAA-TAA
1 TGATGTCATTGCTTACATCATTTAATTAA
75668 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
75693 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 21 0.43
29 28 0.57
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Found at i:91359 original size:9 final size:9
Alignment explanation
Indices: 91347--91381 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
91337 GTTCGGTAAG
91347 TTCAATAGA
1 TTCAATAGA
91356 TTCAATAGA
1 TTCAATAGA
91365 TTCAATAGA
1 TTCAATAGA
91374 TTCAATAG
1 TTCAATAG
91382 CTTAATAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (9 bp):
TTCAATAGA
Done.