Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001954.1 Hibiscus syriacus cultivar Beakdansim tig00003954_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: 44187
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3051 original size:13 final size:13
Alignment explanation
Indices: 3033--3060 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3023 GTATTAGTTG
3033 GCTTAAATAATCT
1 GCTTAAATAATCT
3046 GCTTAAATAATCT
1 GCTTAAATAATCT
3059 GC
1 GC
3061 GATGCAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (13 bp):
GCTTAAATAATCT
Found at i:5956 original size:126 final size:127
Alignment explanation
Indices: 5699--6202 Score: 806
Period size: 126 Copynumber: 4.0 Consensus size: 127
5689 GTACTATTCA
* * * * * *
5699 CGTGAA-G-GCGTTCCCGAGGGCGCGCCTTCAATTATTTTGTCAAAGAATATGTTATTATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
5762 TATTATGTCACTTATGTCCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGT-CCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
*
5825 CGTGAAGGCGCGTTCCCGGGGGCACGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
* *
5890 TATTATGTCACTTATGT-CTCCGGGAACTATTCATGCCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
*
5951 TGTGAAGGCGCGTTCCC-GGGG-ACGTACCTTCCATTATTTTGTCAGAGAATATGTTATCATTAC
1 CGTGAAGGCGCGTTCCCGGGGGCACG--CCTTCCATTATTTTGTCAGAGAATATGTTATCATTAC
*
6014 TCTATTATGTCACTTATGTCCCCC-GGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
64 CCTATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
6077 CGTGAAGGCGCGTTCCTGGGGGCACGCCTTCCATTATTTTGTCAGAAAATATG-TATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
6141 TATTATGTCACTTATGTCCCCCGGGAACTATTCATATCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
6203 TTTAAAGCGC
Statistics
Matches: 351, Mismatches: 19, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
124 3 0.01
125 36 0.10
126 235 0.67
127 8 0.02
128 69 0.20
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:6664 original size:34 final size:34
Alignment explanation
Indices: 6626--6726 Score: 123
Period size: 34 Copynumber: 3.0 Consensus size: 34
6616 GAATTTAATG
*
6626 TTAAATTTCGAATATTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
** * *
6660 TTAAATTTTAAATAATACTATTTTA-ATTTTAATT
1 TTAAATTTCGAATAATA-TAATTTATATTTTAAAT
* *
6694 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
6727 AACATTTATT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
33 5 0.09
34 43 0.80
35 6 0.11
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:9471 original size:60 final size:60
Alignment explanation
Indices: 9360--9480 Score: 149
Period size: 60 Copynumber: 2.0 Consensus size: 60
9350 AGACGTGTCT
* *
9360 CCGGGGATGCGCCTTTCACACGTGGCAACTGAATCATCAAAATAAAGGTAAAGCGCATCC
1 CCGGGGATGCGCCTTTCACACGTGGCAACTCAATCATCAAAATAAAGGTAAAACGCATCC
* * *
9420 CCGGGGATGCGCCTTTTACACGTGGC-A-TCAACTCAACGTAAAATCAA-GTAAAACGCATCC
1 CCGGGGATGCGCCTTTCACACGTGGCAACTCAA-TCATC--AAAATAAAGGTAAAACGCATCC
9480 C
1 C
9481 GGATGCGTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
58 3 0.06
59 5 0.09
60 38 0.72
61 7 0.13
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.19
Consensus pattern (60 bp):
CCGGGGATGCGCCTTTCACACGTGGCAACTCAATCATCAAAATAAAGGTAAAACGCATCC
Found at i:12119 original size:2 final size:2
Alignment explanation
Indices: 12112--12198 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
12102 GGTTGCCCCG
12112 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
12154 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
12196 AT A
1 AT A
12199 ATGTTTTATG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12656 original size:30 final size:30
Alignment explanation
Indices: 12622--12752 Score: 212
Period size: 30 Copynumber: 4.4 Consensus size: 30
12612 GAAAAATTAC
*
12622 AAATTGGTCACTAACT-TTATCATTTGTTAT
1 AAATTGGTCACTAA-TGTTATCGTTTGTTAT
12652 AAATTGGTCACTAATGTTATCGTTTGTTAT
1 AAATTGGTCACTAATGTTATCGTTTGTTAT
* *
12682 AAATTGATCTCTAAT-TTATCGTTTGTTAT
1 AAATTGGTCACTAATGTTATCGTTTGTTAT
12711 AAATTGGTCACTAATGTTATCGTTTGTTAT
1 AAATTGGTCACTAATGTTATCGTTTGTTAT
12741 AAATTGGTCACT
1 AAATTGGTCACT
12753 CGCATTAACA
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
29 28 0.30
30 66 0.70
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (30 bp):
AAATTGGTCACTAATGTTATCGTTTGTTAT
Found at i:12733 original size:59 final size:60
Alignment explanation
Indices: 12622--12752 Score: 219
Period size: 59 Copynumber: 2.2 Consensus size: 60
12612 GAAAAATTAC
*
12622 AAATTGGTCACTAACTTTATCATTTGTTATAAATTGGTCACTAATGTTATCGTTTGTTAT
1 AAATTGATCACTAACTTTATCATTTGTTATAAATTGGTCACTAATGTTATCGTTTGTTAT
* *
12682 AAATTGATCTCTAA-TTTATCGTTTGTTATAAATTGGTCACTAATGTTATCGTTTGTTAT
1 AAATTGATCACTAACTTTATCATTTGTTATAAATTGGTCACTAATGTTATCGTTTGTTAT
*
12741 AAATTGGTCACT
1 AAATTGATCACT
12753 CGCATTAACA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
59 54 0.82
60 12 0.18
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (60 bp):
AAATTGATCACTAACTTTATCATTTGTTATAAATTGGTCACTAATGTTATCGTTTGTTAT
Found at i:14128 original size:30 final size:30
Alignment explanation
Indices: 14094--14194 Score: 157
Period size: 30 Copynumber: 3.4 Consensus size: 30
14084 AATAGCGAGT
*
14094 GACCAATTTGTAACAAATGATAACGTTAGC
1 GACCAATTTATAACAAATGATAACGTTAGC
*
14124 GACCACTTTATAACAAATGATAACGTTAGC
1 GACCAATTTATAACAAATGATAACGTTAGC
* *
14154 GACCAATTTATAACAAATGATAATGTTAGT
1 GACCAATTTATAACAAATGATAACGTTAGC
*
14184 GACCGATTTAT
1 GACCAATTTAT
14195 GATTTTTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (30 bp):
GACCAATTTATAACAAATGATAACGTTAGC
Found at i:17994 original size:11 final size:11
Alignment explanation
Indices: 17978--18002 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17968 TAGAATAAAT
17978 TTTTATTTATG
1 TTTTATTTATG
17989 TTTTATTTATG
1 TTTTATTTATG
18000 TTT
1 TTT
18003 ATATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTATTTATG
Found at i:18009 original size:2 final size:2
Alignment explanation
Indices: 18002--18036 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
17992 TATTTATGTT
18002 TA 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 TA T
18037 GAAAATTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18391 original size:4 final size:4
Alignment explanation
Indices: 18350--18375 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18340 TAAATGTCCA
18350 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
18376 TCATGCGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:19053 original size:16 final size:17
Alignment explanation
Indices: 19025--19058 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
19015 AATAAATTCA
19025 TAATTATTTTTAAAATT
1 TAATTATTTTTAAAATT
19042 TAATTA-TTTTAAAATT
1 TAATTATTTTTAAAATT
19058 T
1 T
19059 TCAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTATTTTTAAAATT
Found at i:23272 original size:3 final size:3
Alignment explanation
Indices: 23266--23292 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
23256 ATAAAAAAAA
23266 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
23293 AATACATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:26031 original size:29 final size:30
Alignment explanation
Indices: 25968--26051 Score: 134
Period size: 29 Copynumber: 2.8 Consensus size: 30
25958 CAAACTAAAT
* *
25968 TGATGTCATTACTTACATCATTTTAATTAA
1 TGATGTCATTGCTTACATCAATTTAATTAA
*
25998 AGATGTCATTGCTTACAT-AATTTAATTAA
1 TGATGTCATTGCTTACATCAATTTAATTAA
26027 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATCAATTTA
26052 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 27 0.55
30 22 0.45
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (30 bp):
TGATGTCATTGCTTACATCAATTTAATTAA
Found at i:30750 original size:29 final size:29
Alignment explanation
Indices: 30715--30796 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
30705 AAACTAAATT
*
30715 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
* *
30744 GATGTCATTGCTTACATAATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
30773 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
30797 GTTAGGTGAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:33275 original size:15 final size:15
Alignment explanation
Indices: 33257--33286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33247 GGGGAGAAAG
33257 AGGAAGGTGAGGGTT
1 AGGAAGGTGAGGGTT
*
33272 AGGAGGGTGAGGGTT
1 AGGAAGGTGAGGGTT
33287 TCCAATGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.57, T:0.20
Consensus pattern (15 bp):
AGGAAGGTGAGGGTT
Found at i:35108 original size:27 final size:27
Alignment explanation
Indices: 35077--35132 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
35067 AGCCCTAATA
35077 AATAATGTAAAACATCATATCTAATCC
1 AATAATGTAAAACATCATATCTAATCC
* *
35104 AATAATGTAAAACGTCGTATCTAATCC
1 AATAATGTAAAACATCATATCTAATCC
35131 AA
1 AA
35133 ATTTTACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (27 bp):
AATAATGTAAAACATCATATCTAATCC
Found at i:35587 original size:21 final size:21
Alignment explanation
Indices: 35561--35618 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
35551 AATTATGTGA
* *
35561 TAGGGTTTATGATTTAAGTTT
1 TAGGGTTTATGGTTTAAGATT
35582 TAGGGTTTATGGTTTAAGATT
1 TAGGGTTTATGGTTTAAGATT
35603 TAGGGTTTATGGTTTA
1 TAGGGTTTATGGTTTA
35619 GGGTTCATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (21 bp):
TAGGGTTTATGGTTTAAGATT
Found at i:35590 original size:7 final size:7
Alignment explanation
Indices: 35561--35634 Score: 58
Period size: 7 Copynumber: 10.6 Consensus size: 7
35551 AATTATGTGA
35561 TAGGGTT
1 TAGGGTT
* *
35568 TATGATT
1 TAGGGTT
* *
35575 TAAGTTT
1 TAGGGTT
35582 TAGGGTT
1 TAGGGTT
*
35589 TATGGTT
1 TAGGGTT
* *
35596 TAAGATT
1 TAGGGTT
35603 TAGGGTT
1 TAGGGTT
*
35610 TATGGTT
1 TAGGGTT
35617 TAGGGTT
1 TAGGGTT
* *
35624 CATGGTT
1 TAGGGTT
35631 TAGG
1 TAGG
35635 ATTCATGGTT
Statistics
Matches: 50, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:35628 original size:14 final size:14
Alignment explanation
Indices: 35601--35646 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
35591 TGGTTTAAGA
*
35601 TTTAGGGTTTATGG
1 TTTAGGGTTCATGG
35615 TTTAGGGTTCATGG
1 TTTAGGGTTCATGG
*
35629 TTTAGGATTCATGG
1 TTTAGGGTTCATGG
35643 TTTA
1 TTTA
35647 ATTTATACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.17, C:0.04, G:0.30, T:0.48
Consensus pattern (14 bp):
TTTAGGGTTCATGG
Found at i:35630 original size:21 final size:21
Alignment explanation
Indices: 35562--35632 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
35552 ATTATGTGAT
* * *
35562 AGGGTTTATGATTTAAGTTTT
1 AGGGTTTATGGTTTAAGATTC
*
35583 AGGGTTTATGGTTTAAGATTT
1 AGGGTTTATGGTTTAAGATTC
* *
35604 AGGGTTTATGGTTTAGGGTTC
1 AGGGTTTATGGTTTAAGATTC
*
35625 ATGGTTTA
1 AGGGTTTA
35633 GGATTCATGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (21 bp):
AGGGTTTATGGTTTAAGATTC
Found at i:35943 original size:15 final size:17
Alignment explanation
Indices: 35909--35944 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
35899 AATGTCAAAT
35909 AATTAAAAACAAGACAC
1 AATTAAAAACAAGACAC
35926 AATT-AAAACAAG-CAC
1 AATTAAAAACAAGACAC
35941 AATT
1 AATT
35945 GAATGAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 8 0.42
17 4 0.21
ACGTcount: A:0.61, C:0.17, G:0.06, T:0.17
Consensus pattern (17 bp):
AATTAAAAACAAGACAC
Found at i:40564 original size:7 final size:7
Alignment explanation
Indices: 40536--40672 Score: 87
Period size: 7 Copynumber: 19.6 Consensus size: 7
40526 TTGCAATGAG
40536 CCCTAAA
1 CCCTAAA
*
40543 -CCTTAA
1 CCCTAAA
*
40549 CCATAAA
1 CCCTAAA
*
40556 TCCTAAA
1 CCCTAAA
*
40563 TCCTAAA
1 CCCTAAA
**
40570 CTATAAA
1 CCCTAAA
40577 CCCTAAA
1 CCCTAAA
***
40584 TATTAAA
1 CCCTAAA
* *
40591 TCATAAA
1 CCCTAAA
*
40598 CACTAAA
1 CCCTAAA
40605 CCCTAAA
1 CCCTAAA
40612 CCCTAAA
1 CCCTAAA
40619 CCCTAAA
1 CCCTAAA
***
40626 TATTAAA
1 CCCTAAA
40633 CCCTAAA
1 CCCTAAA
40640 CCCTAAA
1 CCCTAAA
**
40647 CAATAAAA
1 CCCT-AAA
*
40655 ACCTAAA
1 CCCTAAA
*
40662 TCCTAAA
1 CCCTAAA
40669 CCCT
1 CCCT
40673 TAATCCGATT
Statistics
Matches: 96, Mismatches: 32, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
6 5 0.05
7 87 0.91
8 4 0.04
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (7 bp):
CCCTAAA
Found at i:40581 original size:21 final size:21
Alignment explanation
Indices: 40536--40646 Score: 107
Period size: 21 Copynumber: 5.3 Consensus size: 21
40526 TTGCAATGAG
*
40536 CCCTAAA-CCTTAACCATAAA
1 CCCTAAATCCTAAACCATAAA
* *
40556 TCCTAAATCCTAAACTATAAA
1 CCCTAAATCCTAAACCATAAA
** *
40577 CCCTAAATATTAAATCATAAA
1 CCCTAAATCCTAAACCATAAA
* * *
40598 CACTAAACCCTAAACCCTAAA
1 CCCTAAATCCTAAACCATAAA
** *
40619 CCCTAAATATTAAACCCTAAA
1 CCCTAAATCCTAAACCATAAA
40640 CCCTAAA
1 CCCTAAA
40647 CAATAAAAAC
Statistics
Matches: 72, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
20 6 0.08
21 66 0.92
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
CCCTAAATCCTAAACCATAAA
Found at i:40583 original size:28 final size:29
Alignment explanation
Indices: 40547--40646 Score: 107
Period size: 28 Copynumber: 3.6 Consensus size: 29
40537 CCTAAACCTT
* *
40547 AACCATAAATCCTAAATCCTAAACTA-TA
1 AACCCTAAACCCTAAATCCTAAACTACTA
*** *
40575 AACCCTAAATATTAAATCATAAAC-ACTA
1 AACCCTAAACCCTAAATCCTAAACTACTA
* *
40603 AACCCTAAACCCTAAACCCTAAA-TATTA
1 AACCCTAAACCCTAAATCCTAAACTACTA
40631 AACCCTAAACCCTAAA
1 AACCCTAAACCCTAAA
40647 CAATAAAAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
27 1 0.02
28 59 0.98
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (29 bp):
AACCCTAAACCCTAAATCCTAAACTACTA
Found at i:41350 original size:16 final size:16
Alignment explanation
Indices: 41325--41355 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41315 TTTAAATTTT
*
41325 TTTTTGAGTTTGAGTA
1 TTTTTAAGTTTGAGTA
41341 TTTTTAAGTTTGAGT
1 TTTTTAAGTTTGAGT
41356 TGAGTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.23, T:0.58
Consensus pattern (16 bp):
TTTTTAAGTTTGAGTA
Done.