Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007498.1 Hibiscus syriacus cultivar Beakdansim tig00020752_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: 89169
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5544 original size:68 final size:68
Alignment explanation
Indices: 5430--5566 Score: 179
Period size: 68 Copynumber: 2.0 Consensus size: 68
5420 GGTTTAACAC
* * *
5430 TAGAGTGTACATAAGACACACTTAGTGTAGGTGGTGGGCACTACCTTATGTGTC-ATTCGATTTA
1 TAGAGTGTACATAAAACACACTTAGTGTA-GTGGTAGGCACAACCTTATGTGTCAATTCGATTTA
5494 GCAA
65 GCAA
* *
5498 TAGAGTGTATATAAAAGACACTTAGTTTGTA-TGGTAGGCACAACCTTATGTGTCATATTCGATT
1 TAGAGTGTACATAAAACACACTTAG--TGTAGTGGTAGGCACAACCTTATGTGTCA-ATTCGATT
5562 TAGCA
63 TAGCA
5567 CATTGGAGCA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
68 43 0.72
70 17 0.28
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (68 bp):
TAGAGTGTACATAAAACACACTTAGTGTAGTGGTAGGCACAACCTTATGTGTCAATTCGATTTAG
CAA
Found at i:9786 original size:21 final size:22
Alignment explanation
Indices: 9751--9791 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9741 AAAGTGACTA
*
9751 AACATTTTTAAATCATTTACTC
1 AACATTTTCAAATCATTTACTC
9773 AACA-TTTCAAATCATTTAC
1 AACATTTTCAAATCATTTAC
9792 ACAAAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (22 bp):
AACATTTTCAAATCATTTACTC
Found at i:10059 original size:70 final size:70
Alignment explanation
Indices: 9946--10085 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
9936 CCCCTAAGAC
9946 TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
1 TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
10011 TTTGA
66 TTTGA
10016 TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
1 TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
10081 TTTGA
66 TTTGA
10086 AAGTTGAGCT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (70 bp):
TCCTTTGATGATATTATTGTTCCATCGTGCTCCACGTAACCTCTAACCAATGAACGAAAACACAT
TTTGA
Found at i:12391 original size:19 final size:21
Alignment explanation
Indices: 12356--12395 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
12346 AGGGCCCGAG
12356 TGGTAACTTTCCCCAAAAATA
1 TGGTAACTTTCCCCAAAAATA
12377 TGGTAA-TTT-CCCAAAAATA
1 TGGTAACTTTCCCCAAAAATA
12396 AATTTTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 3 0.16
21 6 0.32
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (21 bp):
TGGTAACTTTCCCCAAAAATA
Found at i:13475 original size:20 final size:20
Alignment explanation
Indices: 13430--13476 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
13420 ATTTTGCTGG
* *
13430 AATTTAATGTTAAAGTGTTT
1 AATTTGATGTTAAAGTGTGT
13450 AATTTGATGTTAGAA-TGTGT
1 AATTTGATGTTA-AAGTGTGT
13470 AATTTGA
1 AATTTGA
13477 CTATTTTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (20 bp):
AATTTGATGTTAAAGTGTGT
Found at i:22546 original size:11 final size:11
Alignment explanation
Indices: 22530--22556 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
22520 AACAGTAAAT
22530 AAAATGAAAAG
1 AAAATGAAAAG
22541 AAAATGAAAAG
1 AAAATGAAAAG
22552 AAAAT
1 AAAAT
22557 AATCCTCACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (11 bp):
AAAATGAAAAG
Found at i:24021 original size:25 final size:24
Alignment explanation
Indices: 23992--24069 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
23982 ACCTTTGTGT
* *
23992 ACTCCAGTATTAGTGCATTTTTTGC
1 ACTCCAGTATTAGTGC-CTTGTTGC
* *
24017 ACTCCTGTTTTAGTGCCTTGTTGC
1 ACTCCAGTATTAGTGCCTTGTTGC
** * * *
24041 ACTCCAACAATAGTGCATTGGTGC
1 ACTCCAGTATTAGTGCCTTGTTGC
24065 ACTCC
1 ACTCC
24070 TATATTATTA
Statistics
Matches: 42, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 28 0.67
25 14 0.33
ACGTcount: A:0.19, C:0.26, G:0.18, T:0.37
Consensus pattern (24 bp):
ACTCCAGTATTAGTGCCTTGTTGC
Found at i:24162 original size:24 final size:24
Alignment explanation
Indices: 24118--24166 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
24108 TGTGCACTAT
*
24118 TGTGTTAGTATCTTTGAGTACTCC
1 TGTGTTAGTATCTTCGAGTACTCC
*
24142 TGTGTTAGTA-CATTCGTGTACTCC
1 TGTGTTAGTATC-TTCGAGTACTCC
24166 T
1 T
24167 CGTACTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.45
Consensus pattern (24 bp):
TGTGTTAGTATCTTCGAGTACTCC
Found at i:42736 original size:30 final size:30
Alignment explanation
Indices: 42702--42765 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
42692 GGAAACATCT
*
42702 GATCTAATACATAACATGGCATAAATTATA
1 GATCTAATACATAACATGACATAAATTATA
* *
42732 GATCTAATGCATAACATGACATACATTATA
1 GATCTAATACATAACATGACATAAATTATA
42762 GATC
1 GATC
42766 CTATTTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.30
Consensus pattern (30 bp):
GATCTAATACATAACATGACATAAATTATA
Found at i:55400 original size:20 final size:21
Alignment explanation
Indices: 55371--55410 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
55361 TGATGTGCTA
55371 TGTTGTAAATTAATGTTAGAG
1 TGTTGTAAATTAATGTTAGAG
*
55392 TGTTG-AAATTGATGTTAGA
1 TGTTGTAAATTAATGTTAGA
55411 AAGTGAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (21 bp):
TGTTGTAAATTAATGTTAGAG
Found at i:60162 original size:21 final size:21
Alignment explanation
Indices: 60132--60173 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60122 AGATCTCTCA
60132 TTTCCTTTCTTTATT-TTCCT
1 TTTCCTTTCTTTATTCTTCCT
*
60152 TTTCCATTTCTTTTTTCTTCCT
1 TTTCC-TTTCTTTATTCTTCCT
60174 CCTCAAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTCCTTTCTTTATTCTTCCT
Found at i:60666 original size:20 final size:20
Alignment explanation
Indices: 60630--60667 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
60620 AGGGTTCAAG
*
60630 TATCGATACTGGATGAATAA
1 TATCGATACTAGATGAATAA
*
60650 TATCGATACTAGTTGAAT
1 TATCGATACTAGATGAAT
60668 TGGGGATAAA
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:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (20 bp):
TATCGATACTAGATGAATAA
Found at i:61962 original size:32 final size:32
Alignment explanation
Indices: 61862--61963 Score: 150
Period size: 32 Copynumber: 3.2 Consensus size: 32
61852 CAGATACTAG
* *
61862 TCAGGTTTGCATTCAGATAATACATAATATGT
1 TCAGGTTTGCATTCAGATAATGCACAATATGT
* * *
61894 TCAAGTTTGCATTTAGATAATGCACAATATGA
1 TCAGGTTTGCATTCAGATAATGCACAATATGT
*
61926 TCAGGTTTGCATTCATATAATGCACAATATGT
1 TCAGGTTTGCATTCAGATAATGCACAATATGT
61958 TCAGGT
1 TCAGGT
61964 CATACGTGTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (32 bp):
TCAGGTTTGCATTCAGATAATGCACAATATGT
Found at i:64364 original size:45 final size:44
Alignment explanation
Indices: 64267--64555 Score: 308
Period size: 45 Copynumber: 6.4 Consensus size: 44
64257 TTCATTTGTA
* * * *
64267 GCATCATTTCATGCTTATAATTCACCGTTATACATTTTCATTTATG
1 GCATCCTTTCATGCCTATAATGCACCGTTATGCA-TTT-ATTTATG
* * * * *
64313 GAATCCTTTTATGCCAATAATGCACCATTATGCAGTTTATTTAAG
1 GCATCCTTTCATGCCTATAATGCACCGTTATGCA-TTTATTTATG
* * *
64358 GCATCCTTTCATGCCGATAATGCAACGTTATGCATCTCATTTATG
1 GCATCCTTTCATGCCTATAATGCACCGTTATGCAT-TTATTTATG
* * * *
64403 GTATTCTTTCATGCCTATAATGCACTGTTATGCATTATATATATG
1 GCATCCTTTCATGCCTATAATGCACCGTTATGCATT-TATTTATG
** * *
64448 ATATCCTTTCATGCCTATAATGCACCGTTATGCATTACATATATG
1 GCATCCTTTCATGCCTATAATGCACCGTTATGCATT-TATTTATG
* *
64493 GCATCCTTTCATGCCTATAATGCACCGTTATGCATTACATATATG
1 GCATCCTTTCATGCCTATAATGCACCGTTATGCATT-TATTTATG
*
64538 GCATCATTTCATGCCTAT
1 GCATCCTTTCATGCCTAT
64556 TCCTACTCTA
Statistics
Matches: 210, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
44 2 0.01
45 179 0.85
46 29 0.14
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (44 bp):
GCATCCTTTCATGCCTATAATGCACCGTTATGCATTTATTTATG
Found at i:64427 original size:90 final size:89
Alignment explanation
Indices: 64267--64555 Score: 346
Period size: 90 Copynumber: 3.2 Consensus size: 89
64257 TTCATTTGTA
* * * * *
64267 GCATCATTTCATGCTTATAATTCACCGTTATACATTTTCATTTATGGAATCCTTTTATGCCAATA
1 GCATCATTTCATGCCTATAATGCACCGTTATGCA--TTCATTTATGGAATCCTTTCATGCCTATA
* * *
64332 ATGCACCATTATGCAGTT-TATTTAAG
64 ATGCACCGTTATGCA-TTATATATATG
* * * * *
64358 GCATCCTTTCATGCCGATAATGCAACGTTATGCATCTCATTTATGGTATTCTTTCATGCCTATAA
1 GCATCATTTCATGCCTATAATGCACCGTTATGCAT-TCATTTATGGAATCCTTTCATGCCTATAA
*
64423 TGCACTGTTATGCATTATATATATG
65 TGCACCGTTATGCATTATATATATG
** * * *
64448 ATATCCTTTCATGCCTATAATGCACCGTTATGCATTACATATATGGCATCCTTTCATGCCTATAA
1 GCATCATTTCATGCCTATAATGCACCGTTATGCATT-CATTTATGGAATCCTTTCATGCCTATAA
*
64513 TGCACCGTTATGCATTACATATATG
65 TGCACCGTTATGCATTATATATATG
64538 GCATCATTTCATGCCTAT
1 GCATCATTTCATGCCTAT
64556 TCCTACTCTA
Statistics
Matches: 169, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
89 4 0.02
90 137 0.81
91 28 0.17
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (89 bp):
GCATCATTTCATGCCTATAATGCACCGTTATGCATTCATTTATGGAATCCTTTCATGCCTATAAT
GCACCGTTATGCATTATATATATG
Found at i:64490 original size:24 final size:24
Alignment explanation
Indices: 64463--64535 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
64453 CTTTCATGCC
64463 TATAATGCACCGTTATGCATTACA
1 TATAATGCACCGTTATGCATTACA
* *
64487 TAT-ATGGCATCC-TT-T-CA-TGCC
1 TATAAT-GCA-CCGTTATGCATTACA
64508 TATAATGCACCGTTATGCATTACA
1 TATAATGCACCGTTATGCATTACA
64532 TATA
1 TATA
64536 TGGCATCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 5 0.13
23 5 0.13
24 14 0.37
25 2 0.05
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (24 bp):
TATAATGCACCGTTATGCATTACA
Found at i:64501 original size:135 final size:136
Alignment explanation
Indices: 64267--64555 Score: 363
Period size: 135 Copynumber: 2.1 Consensus size: 136
64257 TTCATTTGTA
* * * * *
64267 GCATCATTTCATGCTTATAATTCACCGTTATACATTTTCATTTATGGAATCCTTTTATGCCAATA
1 GCATCATTTCATGCCTATAATGCACCGTTATACATTATCATATATGGAATCCTTTCATGCCAATA
* *
64332 ATGCACCATTATGCAGTTTATTTAAGGCATCCTTTCATGCCGATAATGCAACGTTATGCATCT-C
66 ATGCACCATTATGCAGTTCATATAAGGCATCCTTTCATGCCGATAATGCAACGTTATGCAT-TAC
*
64396 ATTTATG
130 ATATATG
* * * *
64403 GTATTC-TTTCATGCCTATAATGCACTGTTATGCATTAT-ATATAT-GATATCCTTTCATGCCTA
1 GCA-TCATTTCATGCCTATAATGCACCGTTATACATTATCATATATGGA-ATCCTTTCATGCCAA
* * * *
64465 TAATGCACCGTTATGCA-TTACATATATGGCATCCTTTCATGCCTATAATGCACCGTTATGCATT
64 TAATGCACCATTATGCAGTT-CATATAAGGCATCCTTTCATGCCGATAATGCAACGTTATGCATT
64529 ACATATATG
128 ACATATATG
64538 GCATCATTTCATGCCTAT
1 GCATCATTTCATGCCTAT
64556 TCCTACTCTA
Statistics
Matches: 131, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
134 7 0.05
135 93 0.71
136 29 0.22
137 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.39
Consensus pattern (136 bp):
GCATCATTTCATGCCTATAATGCACCGTTATACATTATCATATATGGAATCCTTTCATGCCAATA
ATGCACCATTATGCAGTTCATATAAGGCATCCTTTCATGCCGATAATGCAACGTTATGCATTACA
TATATG
Found at i:64511 original size:21 final size:21
Alignment explanation
Indices: 64487--64555 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 21
64477 ATGCATTACA
64487 TATATGGCATCCTTTCATGCC
1 TATATGGCATCCTTTCATGCC
* *
64508 TATAAT-GCA-CCGTTATGCATTACA
1 TAT-ATGGCATCC-TT-T-CA-TGCC
*
64532 TATATGGCATCATTTCATGCC
1 TATATGGCATCCTTTCATGCC
64553 TAT
1 TAT
64556 TCCTACTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 14
0.65 0.09 0.25
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
22 5 0.14
23 5 0.14
24 10 0.28
25 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (21 bp):
TATATGGCATCCTTTCATGCC
Found at i:65013 original size:53 final size:52
Alignment explanation
Indices: 64955--65214 Score: 175
Period size: 53 Copynumber: 5.2 Consensus size: 52
64945 TTTTTATACT
*
64955 ATGGTATCGACACTCCTTTTCAGTATCGATACCATTTCTATATTCTGTAATCC
1 ATGGTATCGATACTCCTTTTCAGTATCGATACCATTTCTATATT-TGTAATCC
* *
65008 ATGGTATCGATACCTTTCTTTT-AGTATCGATA-C--TTCTATA----T-AT-T
1 ATGGTATCGATA-C-TCCTTTTCAGTATCGATACCATTTCTATATTTGTAATCC
* *
65052 ATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATTTTGTAATCC
1 ATGGTATCGATACTCCTTTTCAGTATCGATACCATTTCTATA-TTTGTAATCC
*
65105 ATGGTATCGATA--CCTTTCTCTTAGTATCGATA-CA--TCTATA----T-AT-T
1 ATGGTATCGATACTCCTTT-TC--AGTATCGATACCATTTCTATATTTGTAATCC
* * * * * * *
65149 ATGGAACCGATACTCCCTTTCAATATCGATGCCATTTCTACATTCTGGAATCC
1 ATGGTATCGATACTCCTTTTCAGTATCGATACCATTTCTATATT-TGTAATCC
*
65202 CTGGTATCGATAC
1 ATGGTATCGATAC
65215 CTTTCTCTTA
Statistics
Matches: 158, Mismatches: 21, Indels: 56
0.67 0.09 0.24
Matches are distributed among these distances:
42 5 0.03
43 19 0.12
44 24 0.15
45 6 0.04
46 18 0.11
51 18 0.11
52 6 0.04
53 35 0.22
54 21 0.13
55 6 0.04
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (52 bp):
ATGGTATCGATACTCCTTTTCAGTATCGATACCATTTCTATATTTGTAATCC
Found at i:65040 original size:54 final size:53
Alignment explanation
Indices: 64970--65137 Score: 185
Period size: 54 Copynumber: 3.3 Consensus size: 53
64960 ATCGACACTC
64970 CTTTTCAGTATCGATACCATTTCTATATTCTGTAATCCATGGTATCGATACCTTT
1 CTTTT-AGTATCGATACCATTTCTATATT-TGTAATCCATGGTATCGATACCTTT
* * **
65025 CTTTTAGTATCGATA-C--TTCTATA----T-AT-TATGGTACCGATA-CTCC
1 CTTTTAGTATCGATACCATTTCTATATTTGTAATCCATGGTATCGATACCTTT
*
65068 CTTTCAGTATCGATACCATTTCTATATTTTGTAATCCATGGTATCGATACCTTT
1 CTTTTAGTATCGATACCATTTCTATA-TTTGTAATCCATGGTATCGATACCTTT
*
65122 CTCTTAGTATCGATAC
1 CTTTTAGTATCGATAC
65138 ATCTATATAT
Statistics
Matches: 91, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
43 16 0.18
44 12 0.13
45 2 0.02
46 8 0.09
51 8 0.09
52 2 0.02
53 12 0.13
54 26 0.29
55 5 0.05
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.43
Consensus pattern (53 bp):
CTTTTAGTATCGATACCATTTCTATATTTGTAATCCATGGTATCGATACCTTT
Found at i:65080 original size:97 final size:97
Alignment explanation
Indices: 64936--65234 Score: 449
Period size: 97 Copynumber: 3.1 Consensus size: 97
64926 CTCTACCATG
* * * * *
64936 GTATCGATA-TT-TTTATACTATGGTATCGACACTCCTTTTCAGTATCGATACCATTTCTATATT
1 GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
*
64999 CTGTAATCCATGGTATCGATACCTTTCTTTTA
66 CTGTAATCCATGGTATCGATACCTTTCTCTTA
65031 GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
1 GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
*
65096 TTGTAATCCATGGTATCGATACCTTTCTCTTA
66 CTGTAATCCATGGTATCGATACCTTTCTCTTA
* * * * *
65128 GTATCGATACATCTATATATTATGGAACCGATACTCCCTTTCAATATCGATGCCATTTCTACATT
1 GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
* *
65193 CTGGAATCCCTGGTATCGATACCTTTCTCTTA
66 CTGTAATCCATGGTATCGATACCTTTCTCTTA
*
65225 ATATCGATAC
1 GTATCGATAC
65235 ATACAGAAAT
Statistics
Matches: 186, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
95 9 0.05
96 2 0.01
97 175 0.94
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (97 bp):
GTATCGATACTTCTATATATTATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTATATT
CTGTAATCCATGGTATCGATACCTTTCTCTTA
Found at i:77172 original size:46 final size:46
Alignment explanation
Indices: 77119--77209 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
77109 ATTATACTTT
* **
77119 ATTTTCATATATAGCATCATTTCATGCTTATAATGCACCGTTATGC
1 ATTTTCATATATAGCATCATTTCACGCCAATAATGCACCGTTATGC
* * * * *
77165 ATTTTCATTTATGGTATCCTTTTACGCCAATAATGCACCGTTATG
1 ATTTTCATATATAGCATCATTTCACGCCAATAATGCACCGTTATG
77210 AAATTCATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (46 bp):
ATTTTCATATATAGCATCATTTCACGCCAATAATGCACCGTTATGC
Found at i:77243 original size:45 final size:46
Alignment explanation
Indices: 77148--77246 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 46
77138 TTTCATGCTT
** * * *
77148 ATAATGCACCGTTATGCATTTTCATTTATGGTATCCTTTTACGCCA
1 ATAATGCACCGTTATGCAAATTCATTTATGGCATCCTTTCACACCA
* *
77194 ATAATGCACCGTTATG-AAATTCATTTATGGCATCCTTTCATACCG
1 ATAATGCACCGTTATGCAAATTCATTTATGGCATCCTTTCACACCA
77239 ATAATGCA
1 ATAATGCA
77247 TCTAATTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 30 0.65
46 16 0.35
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.37
Consensus pattern (46 bp):
ATAATGCACCGTTATGCAAATTCATTTATGGCATCCTTTCACACCA
Found at i:77292 original size:45 final size:45
Alignment explanation
Indices: 77254--77410 Score: 201
Period size: 45 Copynumber: 3.5 Consensus size: 45
77244 GCATCTAATT
* *
77254 TATGGTATCATTTCAAGCCTATAATGCACCGTTATGCATTACATA
1 TATGGTATCCTTTCATGCCTATAATGCACCGTTATGCATTACATA
* * * *
77299 CAT-GTCATCCTTTCATGACTATAACGCACCG-TACTGAATTACATA
1 TATGGT-ATCCTTTCATGCCTATAATGCACCGTTA-TGCATTACATA
* *
77344 TATGGAATCCTTTCATGCCTATAATGTACCGTTATGCATTACATA
1 TATGGTATCCTTTCATGCCTATAATGCACCGTTATGCATTACATA
*
77389 TATGGCATCCTTTCATGCCTAT
1 TATGGTATCCTTTCATGCCTAT
77411 TCCTACTATA
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
44 4 0.04
45 88 0.93
46 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (45 bp):
TATGGTATCCTTTCATGCCTATAATGCACCGTTATGCATTACATA
Found at i:77308 original size:80 final size:83
Alignment explanation
Indices: 77171--77405 Score: 237
Period size: 80 Copynumber: 2.8 Consensus size: 83
77161 ATGCATTTTC
* * * * *
77171 ATTTATGGTATCCTTTTACGCCAATAATGCACCGTTATGAAATT-CATTTATGGCATCCTTTCAT
1 ATTTATGGTATCCTTTCAAGCCTATAATGCACCGTTATG-CATTACATATATGGCATCCTTTCAT
*
77235 -ACCGATAATGCA-T-CT-A
65 GA-CGATAACGCACTACTGA
* * *
77251 ATTTATGGTATCATTTCAAGCCTATAATGCACCGTTATGCATTACATACATGTCATCCTTTCATG
1 ATTTATGGTATCCTTTCAAGCCTATAATGCACCGTTATGCATTACATATATGGCATCCTTTCATG
*
77316 ACTATAACGCACCGTACTGA
66 ACGATAACGCA-C-TACTGA
* * *
77336 ATTACATATATGGAATCCTTTCATGCCTATAATGTACCGTTATGCATTACATATATGGCATCCTT
1 A-T---T-TATGGTATCCTTTCAAGCCTATAATGCACCGTTATGCATTACATATATGGCATCCTT
77401 TCATG
61 TCATG
77406 CCTATTCCTA
Statistics
Matches: 127, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
79 3 0.02
80 60 0.47
81 1 0.01
83 1 0.01
84 2 0.02
85 2 0.02
86 1 0.01
89 1 0.01
90 56 0.44
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.37
Consensus pattern (83 bp):
ATTTATGGTATCCTTTCAAGCCTATAATGCACCGTTATGCATTACATATATGGCATCCTTTCATG
ACGATAACGCACTACTGA
Found at i:77368 original size:125 final size:126
Alignment explanation
Indices: 77134--77369 Score: 291
Period size: 125 Copynumber: 1.9 Consensus size: 126
77124 CATATATAGC
* * * ** * * *
77134 ATCATTTCATGCTTATAATGCACCGTTATGCATTTTCATTTATGGTATCCTTTTACGCCAATAAT
1 ATCATTTCAAGCCTATAATGCACCGTTATGCATTTACATACATGGTATCCTTTCACGACAATAAC
* *
77199 GCACCGTTATGAAATTCATTTATGGCATCCTTTCATACCGATAATGCATCTAATTTATGGT
66 GCACCGTTATGAAATTCATATATGGAATCCTTTCATACCGATAATGCATCTAATTTATGGT
* *
77260 ATCATTTCAAGCCTATAATGCACCGTTATGCA-TTACATACAT-GTCATCCTTTCATGACTATAA
1 ATCATTTCAAGCCTATAATGCACCGTTATGCATTTACATACATGGT-ATCCTTTCACGACAATAA
* *
77323 CGCACCG-TACTG-AATTACATATATGGAATCCTTTCATGCCTATAATG
65 CGCACCGTTA-TGAAATT-CATATATGGAATCCTTTCATACCGATAATG
77370 TACCGTTATG
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
124 8 0.09
125 55 0.59
126 30 0.32
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (126 bp):
ATCATTTCAAGCCTATAATGCACCGTTATGCATTTACATACATGGTATCCTTTCACGACAATAAC
GCACCGTTATGAAATTCATATATGGAATCCTTTCATACCGATAATGCATCTAATTTATGGT
Found at i:78016 original size:97 final size:97
Alignment explanation
Indices: 77843--78115 Score: 384
Period size: 97 Copynumber: 2.8 Consensus size: 97
77833 TATGGTACTA
** *
77843 ATACTCCCTTTCAGTATCGATACCATTTCTACCCTCTGTAATCCATGGTATCGATATCTTTCTCT
1 ATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGTAATCCATGGTATCGATACCTTTCTCT
*
77908 TAGTATTGATACTTCTATATATTATGATACCG
66 TAATATTGATACTTCTATATATTATGATACCG
* * * *
77940 ATACTCCCTTTCAGTATCGATACGATTTCTAAATTCTATAATGCATGGTATCGATACCTTTCTCT
1 ATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGTAATCCATGGTATCGATACCTTTCTCT
* * *
78005 TACTATCGATACTTCTATATATTATGGTACCG
66 TAATATTGATACTTCTATATATTATGATACCG
* * * * * * *
78037 ATACTCCCTTTTAGTATCTATACCATTTCTACATTCTGGAATCCCTGGTATCAATACATTTCTGT
1 ATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGTAATCCATGGTATCGATACCTTTCTCT
78102 TAATATTGATACTT
66 TAATATTGATACTT
78116 ACAACAATAT
Statistics
Matches: 153, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
97 153 1.00
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.41
Consensus pattern (97 bp):
ATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGTAATCCATGGTATCGATACCTTTCTCT
TAATATTGATACTTCTATATATTATGATACCG
Found at i:85328 original size:29 final size:29
Alignment explanation
Indices: 85292--85371 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 29
85282 AAAACATGAT
*
85292 AAGATATAATCCCATGCAGAATCAGAATG
1 AAGATATAATCCCATGCAAAATCAGAATG
* * * *
85321 AATATATAATACAATGCAAAATCAGGATG
1 AAGATATAATCCCATGCAAAATCAGAATG
** *
85350 GGGATATAATCCCATTCAAAAT
1 AAGATATAATCCCATGCAAAAT
85372 TAGGACATGA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (29 bp):
AAGATATAATCCCATGCAAAATCAGAATG
Found at i:85424 original size:29 final size:28
Alignment explanation
Indices: 85280--85431 Score: 81
Period size: 29 Copynumber: 5.3 Consensus size: 28
85270 GGATCCTACA
* *
85280 CAAAAACATGATAAGATATAATCCCATG
1 CAAAATCATGATAAGATTTAATCCCATG
* * * * *
85308 CAGAATCA-GAATGAATATATAATACAATG
1 CAAAATCATG-AT-AAGATTTAATCCCATG
* ** * *
85337 CAAAATCAGGATGGGGATATAATCCCATT
1 CAAAATCATGAT-AAGATTTAATCCCATG
* * * * **
85366 CAAAATTAGGACATGATTTAATCCTGTG
1 CAAAATCATGATAAGATTTAATCCCATG
*
85394 CAGAATCATGATAAGAATTTAATCCCATG
1 CAAAATCATGATAAG-ATTTAATCCCATG
*
85423 CATAATCAT
1 CAAAATCAT
85432 AAATGCATTA
Statistics
Matches: 92, Mismatches: 28, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
27 1 0.01
28 28 0.30
29 62 0.67
30 1 0.01
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.26
Consensus pattern (28 bp):
CAAAATCATGATAAGATTTAATCCCATG
Found at i:85490 original size:2 final size:2
Alignment explanation
Indices: 85483--85508 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
85473 CATAAATAAG
85483 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
85509 TCAATTTACG
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:85895 original size:13 final size:13
Alignment explanation
Indices: 85877--85902 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
85867 TTGAAAACAA
85877 AAACGAACTAAAG
1 AAACGAACTAAAG
85890 AAACGAACTAAAG
1 AAACGAACTAAAG
85903 TCATTGTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (13 bp):
AAACGAACTAAAG
Done.