Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003038.1 Hibiscus syriacus cultivar Beakdansim tig00006319_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: 82249
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:384 original size:15 final size:17
Alignment explanation
Indices: 350--389 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
340 TAAATGTAAA
*
350 AAAATATTAAATTATTT
1 AAAATTTTAAATTATTT
367 AAAATTTTAAA-T-TTT
1 AAAATTTTAAATTATTT
382 AAAATTTT
1 AAAATTTT
390 TTCTTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAATTTTAAATTATTT
Found at i:9596 original size:3 final size:3
Alignment explanation
Indices: 9590--9663 Score: 109
Period size: 3 Copynumber: 25.7 Consensus size: 3
9580 ATAATAATAA
9590 TAT TAT TAT TAT TA- TAT TAT T-T TA- TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
9635 TAT TAT TAT TAT TAA TAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
9664 CTACATGCCC
Statistics
Matches: 66, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
2 6 0.09
3 60 0.91
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:11067 original size:30 final size:32
Alignment explanation
Indices: 11032--11102 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
11022 ATTTAGTCAC
* *
11032 TAGTTTTAATATTTTCATTTA-TTTAATTATA
1 TAGTTTTAATATTTTCATATATTTTAAATATA
* *
11063 -AGTTTT-ATTTTTTTATATATTTTAAATATA
1 TAGTTTTAATATTTTCATATATTTTAAATATA
11093 TAGTTTTAAT
1 TAGTTTTAAT
11103 TTCATTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 10 0.30
30 15 0.45
31 6 0.18
32 2 0.06
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (32 bp):
TAGTTTTAATATTTTCATATATTTTAAATATA
Found at i:11119 original size:25 final size:25
Alignment explanation
Indices: 11091--11138 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
11081 ATTTTAAATA
11091 TATAGTTTTAATTTCAT-TGTTTAGT
1 TATA-TTTTAATTTCATATGTTTAGT
*
11116 TATATTTTAATTTTATATGTTTA
1 TATATTTTAATTTCATATGTTTA
11139 TTTTTAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.62
Consensus pattern (25 bp):
TATATTTTAATTTCATATGTTTAGT
Found at i:11381 original size:20 final size:21
Alignment explanation
Indices: 11347--11394 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
11337 GCAACTCGAT
*
11347 AATATTTTGA-TTTTTTAAATA
1 AATATTTTGACTTTTAT-AATA
11368 AATATTTT-ACTTTTATAATA
1 AATATTTTGACTTTTATAATA
*
11388 TATATTT
1 AATATTT
11395 ATCTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
AATATTTTGACTTTTATAATA
Found at i:12075 original size:28 final size:27
Alignment explanation
Indices: 12043--12096 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
12033 TAATTCTTTC
*
12043 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
**
12071 TTTTCCTAATATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
12097 TTATTAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:12104 original size:24 final size:22
Alignment explanation
Indices: 12065--12119 Score: 58
Period size: 24 Copynumber: 2.5 Consensus size: 22
12055 TTATATATAC
*
12065 TTATTATTTTCCTAATATTTATA
1 TTATTATTTTACTAATATTT-TA
* *
12088 TATATTATTTTATTAATGTTTTA
1 T-TATTATTTTACTAATATTTTA
12111 TT-TTATTTT
1 TTATTATTTT
12120 TAATGTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 7 0.25
22 1 0.04
23 4 0.14
24 16 0.57
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTATTTTACTAATATTTTA
Found at i:16995 original size:15 final size:14
Alignment explanation
Indices: 16979--17020 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 14
16969 TTGTAGAAGA
16979 AAAAAAGGAAAAAG
1 AAAAAAGGAAAAAG
16993 -AAAAAGGAAAAAAGG
1 AAAAAAGG-AAAAA-G
17008 AAAAAAGGAAAAA
1 AAAAAAGGAAAAA
17021 AATAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
14 5 0.20
15 6 0.24
16 7 0.28
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAAAGGAAAAAG
Found at i:17004 original size:8 final size:8
Alignment explanation
Indices: 16979--17021 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
16969 TTGTAGAAGA
16979 AAAAAAGG
1 AAAAAAGG
16987 -AAAAA-G
1 AAAAAAGG
16993 -AAAAAGG
1 AAAAAAGG
17000 AAAAAAGG
1 AAAAAAGG
17008 AAAAAAGG
1 AAAAAAGG
17016 AAAAAA
1 AAAAAA
17022 ATAAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.18
7 6 0.18
8 21 0.64
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:17027 original size:8 final size:8
Alignment explanation
Indices: 17016--17053 Score: 69
Period size: 8 Copynumber: 4.9 Consensus size: 8
17006 GGAAAAAAGG
17016 AAAAAAAT
1 AAAAAAAT
17024 AAAAAAAT
1 AAAAAAAT
17032 AAAAAAAT
1 AAAAAAAT
17040 -AAAAAAT
1 AAAAAAAT
17047 AAAAAAA
1 AAAAAAA
17054 ACTTGAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Found at i:17027 original size:16 final size:16
Alignment explanation
Indices: 16993--17045 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
16983 AAGGAAAAAG
**
16993 AAAAAGGAAAAAAGGA
1 AAAAAGGAAAAAAATA
17009 AAAAAGGAAAAAAATA
1 AAAAAGGAAAAAAATA
**
17025 AAAAAATAAAAAAATA
1 AAAAAGGAAAAAAATA
17041 AAAAA
1 AAAAA
17046 TAAAAAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAAGGAAAAAAATA
Found at i:17054 original size:16 final size:16
Alignment explanation
Indices: 17016--17053 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
17006 GGAAAAAAGG
17016 AAAAAAATAAAAAAAT
1 AAAAAAATAAAAAAAT
17032 AAAAAAAT-AAAAAAT
1 AAAAAAATAAAAAAAT
17047 AAAAAAA
1 AAAAAAA
17054 ACTTGAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (16 bp):
AAAAAAATAAAAAAAT
Found at i:20425 original size:75 final size:75
Alignment explanation
Indices: 20346--20524 Score: 196
Period size: 75 Copynumber: 2.4 Consensus size: 75
20336 TTTTAACATC
* * * * *
20346 TGTATCAGTAAATGTTGGGGTATGCTGAAAACCCCTTTCAATCAGAATCAGTAATACTGATGCAT
1 TGTATCAGCAAATGCTGGGGCATGCTGAAAACCCCTTTCAAACAGAATCAGGAATACTGATGCAT
20411 TTTGAACGTT
66 TTTGAACGTT
* * * * * * ** * *
20421 TGTATAAGCCAATGCTAGGGCATGCTAAAAACCCTTTTCAAACATAATCAGGAATGTTGGTGTAT
1 TGTATCAGCAAATGCTGGGGCATGCTGAAAACCCCTTTCAAACAGAATCAGGAATACTGATGCAT
20486 TTTGAACGTT
66 TTTGAACGTT
** *
20496 CATATCAGCAAATGCTGGGGCATACTGAA
1 TGTATCAGCAAATGCTGGGGCATGCTGAA
20525 GGCCCACTTC
Statistics
Matches: 82, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
75 82 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (75 bp):
TGTATCAGCAAATGCTGGGGCATGCTGAAAACCCCTTTCAAACAGAATCAGGAATACTGATGCAT
TTTGAACGTT
Found at i:22349 original size:113 final size:112
Alignment explanation
Indices: 22127--22714 Score: 391
Period size: 123 Copynumber: 5.1 Consensus size: 112
22117 TTAACAAAGA
* * * *
22127 TTCGAATTCATCACTTGATGGATCAACTTTTCCAGA-AGAGTTCATAATGAGAAGAACTTATCTG
1 TTCGAATTCATCACTCGATGAATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTTATCTG
* * * *
22191 AAGAAGAAAAAGAAGCTCATAATGAGAAGAACTTGTTTAACCTTTTGC
66 AAGAAGGAGAA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * *
22239 TT-TAATTCATCACTCGATGAATTAGCATTGCCA-AGTAGAGTTCATAATGAGAAAAACTCATCT
1 TTCGAATTCATCACTCGATGAATCAACATTGCCAGAG-AGAGTTCATAATGAGAAGAACTTATCT
*
22302 GAAGAAGGGAGAATAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-
65 GAAGAA-GGAGAA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * ** * *
22351 TTCGAATTCATCACTTGATGGATCAACTTTTTCAGAGAAAGTTCATCATGAGAAGAACTTATCTG
1 TTCGAATTCATCACTCGATGAATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTTATCTG
*
22416 AAG-A-G-G--AAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
66 AAGAAGGAGAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * *
22458 TT-G-ACTCTATCACAAAAGAAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGA
1 TTCGAATTC-ATCAC---------TCGAT--GAATCAACATTGCCAGAGAGAGTTCATAATGAGA
* * *
22521 AGAACTTATCTGAAG-AGGAATAAGAAGTTCATAATGAGAATAGCTTGTTCAACCTTTTGC
54 AGAACTTATCTGAAGAAGG-AGAA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * * * *
22581 TT-G-ACTCTATCACAGAAGGAGATAGATCATCATCAACATTTCCATATAAAGTTTATAATGAGA
1 TTCGAATTC-ATCAC---------TCGATGA--ATCAACATTGCCAGAGAGAGTTCATAATGAGA
* * * *
22644 AGAACTCATCTGAAGAATGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTTAT-C
54 AGAACTTATCTGAAGAAGGAGAA-AAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
22703 TT-G-ATTCATCAC
1 TTCGAATTCATCAC
22715 ATATGGAGAT
Statistics
Matches: 397, Mismatches: 52, Indels: 45
0.80 0.11 0.09
Matches are distributed among these distances:
105 3 0.01
106 39 0.10
107 2 0.01
109 1 0.00
110 2 0.01
111 24 0.06
112 36 0.09
113 86 0.22
114 2 0.01
115 4 0.01
117 47 0.12
118 1 0.00
121 5 0.01
122 7 0.02
123 136 0.34
124 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (112 bp):
TTCGAATTCATCACTCGATGAATCAACATTGCCAGAGAGAGTTCATAATGAGAAGAACTTATCTG
AAGAAGGAGAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:22594 original size:123 final size:120
Alignment explanation
Indices: 22372--22715 Score: 464
Period size: 123 Copynumber: 2.9 Consensus size: 120
22362 CACTTGATGG
* *
22372 ATCAACTTTTTCAGAGAAAGTTCATCATGAGAAGAACTTATCTGAAGAG---GAAGTTCATAATG
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAAAGAAGTTCATAATG
22434 AGAAGAGCTTGTTCAACCTTTTGCTTGACTCTATCACAAAAGAAGATAGATCAGC
66 AGAAGAGCTTGTTCAACCTTTTGCTTGACTCTATCACAAAAGAAGATAGATCAGC
22489 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAATAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA-G-A-AAGAAGTTCATA
* * * *
22554 ATGAGAATAGCTTGTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCATC
63 ATGAGAAGAGCTTGTTCAACCTTTTGCTTGACTCTATCACAAAAGAAGATAGATCAGC
* * * * *
22612 ATCAACATTTCCATATAAAGTTTATAATGAGAAGAACTCATCTGAAGAATGAGAAGAAGTTCATA
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-A-GA-AAGAAGTTCATA
* * * *
22677 ATGAGAAGAACTTGTTCGACCTTAT-CTTGATTC-ATCACA
63 ATGAGAAGAGCTTGTTCAACCTTTTGCTTGACTCTATCACA
22716 TATGGAGATT
Statistics
Matches: 202, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
117 46 0.23
118 1 0.00
121 6 0.03
122 7 0.03
123 140 0.69
124 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (120 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGAAAGAAGTTCATAATG
AGAAGAGCTTGTTCAACCTTTTGCTTGACTCTATCACAAAAGAAGATAGATCAGC
Found at i:23056 original size:3 final size:3
Alignment explanation
Indices: 23050--23127 Score: 99
Period size: 3 Copynumber: 27.0 Consensus size: 3
23040 CCATTTGTTG
* * *
23050 TTA TTA TTA TTA TTA ATA ATA ATA TTA TTA TTA -TA TTA TT- TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
23095 CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
23128 CTAAAGGCCC
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
2 6 0.09
3 63 0.91
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:24533 original size:30 final size:32
Alignment explanation
Indices: 24498--24568 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
24488 ATTTAGTCAC
* *
24498 TAGTTTTAATATTTTCATTTA-TTTAATTATA
1 TAGTTTTAATATTTTCATATATTTTAAATATA
* *
24529 -AGTTTT-ATTTTTTTATATATTTTAAATATA
1 TAGTTTTAATATTTTCATATATTTTAAATATA
24559 TAGTTTTAAT
1 TAGTTTTAAT
24569 TTCATTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 10 0.30
30 15 0.45
31 6 0.18
32 2 0.06
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.62
Consensus pattern (32 bp):
TAGTTTTAATATTTTCATATATTTTAAATATA
Found at i:24585 original size:25 final size:25
Alignment explanation
Indices: 24557--24604 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
24547 ATTTTAAATA
24557 TATAGTTTTAATTTCAT-TGTTTAGT
1 TATA-TTTTAATTTCATATGTTTAGT
*
24582 TATATTTTAATTTTATATGTTTA
1 TATATTTTAATTTCATATGTTTA
24605 TTTTTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.62
Consensus pattern (25 bp):
TATATTTTAATTTCATATGTTTAGT
Found at i:24619 original size:15 final size:14
Alignment explanation
Indices: 24581--24631 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
24571 CATTGTTTAG
24581 TTATAT-TTTAATT
1 TTATATATTTAATT
* *
24594 TTATATGTTTATTT
1 TTATATATTTAATT
24608 TTAATATATTTAATT
1 TT-ATATATTTAATT
24623 ATTAT-TATT
1 -TTATATATT
24632 ATTATTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 6 0.19
14 12 0.38
15 12 0.38
16 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:34314 original size:2 final size:2
Alignment explanation
Indices: 34309--34352 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
34299 TACATATGAA
*
34309 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG 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
34351 AT
1 AT
34353 CTTTTACATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36341 original size:16 final size:16
Alignment explanation
Indices: 36320--36350 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
36310 TAATATTGAA
36320 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
36336 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
36351 AAATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:37422 original size:18 final size:18
Alignment explanation
Indices: 37399--37451 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 18
37389 TTGTCTCTTC
37399 TTTAATTTTATATAATTT
1 TTTAATTTTATATAATTT
*
37417 TTTAATTAAATTTCTATAATTT
1 TTTAA-T---TTTATATAATTT
37439 TTTAATTTTATAT
1 TTTAATTTTATAT
37452 TAATCGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 11 0.38
19 1 0.03
21 1 0.03
22 16 0.55
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAATTTTATATAATTT
Found at i:37425 original size:22 final size:22
Alignment explanation
Indices: 37400--37445 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
37390 TGTCTCTTCT
*
37400 TTAATTTTATATAATTTTTTAA
1 TTAAATTTATATAATTTTTTAA
*
37422 TTAAATTTCTATAATTTTTTAA
1 TTAAATTTATATAATTTTTTAA
37444 TT
1 TT
37446 TTATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TTAAATTTATATAATTTTTTAA
Found at i:38851 original size:18 final size:17
Alignment explanation
Indices: 38830--38863 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38820 CTATACTATT
38830 ATTATATACTATATTTTC
1 ATTAT-TACTATATTTTC
*
38848 ATTATTATTATATTTT
1 ATTATTACTATATTTT
38864 ATTCCTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATTACTATATTTTC
Found at i:39050 original size:19 final size:19
Alignment explanation
Indices: 39026--39073 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
39016 TATGTATATT
39026 CTTTATATTTTTTCATTTA
1 CTTTATATTTTTTCATTTA
*
39045 CTTTAT-TTATTTTTATTTA
1 CTTTATATT-TTTTCATTTA
* *
39064 TTTTTTATTT
1 CTTTATATTT
39074 ATCTCTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (19 bp):
CTTTATATTTTTTCATTTA
Found at i:39057 original size:21 final size:18
Alignment explanation
Indices: 39031--39073 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
39021 ATATTCTTTA
39031 TATTTTTTCATTTACTTTATT
1 TATTTTTT-ATTTA-TTT-TT
39052 TA-TTTTTATTTATTTTT
1 TATTTTTTATTTATTTTT
39069 TATTT
1 TATTT
39074 ATCTCTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
19 5 0.24
20 5 0.24
21 2 0.10
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTTTATTTATTTTT
Found at i:39070 original size:11 final size:11
Alignment explanation
Indices: 39046--39075 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
39036 TTTCATTTAC
39046 TTTATTTA-TT
1 TTTATTTATTT
39056 TTTATTTATTT
1 TTTATTTATTT
39067 TTTATTTAT
1 TTTATTTAT
39076 CTCTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:39178 original size:141 final size:144
Alignment explanation
Indices: 38943--39207 Score: 482
Period size: 141 Copynumber: 1.9 Consensus size: 144
38933 TATATACATG
38943 ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAACATATATTTTTTTCTTT
1 ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAACA-ATATTTTTTTCTTT
*
39008 TATTATTCTATGTATATTCTTTATATTTTTTCATTTACTTTATTTATTTTTATT-TATTTTTTAT
65 TATTATTATATGTATATTCTTTATATTTTTTCATTTACTTTATTTATTTTTATTCTATTTTTTAT
39072 TTATCTCTATATATA
130 TTATCTCTATATATA
39087 ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAAC-AT-TTTTTTTCTTTT
1 ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAACAATATTTTTTTCTTTT
*
39150 ATTATTATATGTATATTCTTTATTTTTTTTCATTTACTTTATTTATTTTTATTCTATT
66 ATTATTATATGTATATTCTTTATATTTTTTCATTTACTTTATTTATTTTTATTCTATT
39208 GCGTTTCCTT
Statistics
Matches: 118, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
141 63 0.53
142 6 0.05
144 49 0.42
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.62
Consensus pattern (144 bp):
ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAACAATATTTTTTTCTTTT
ATTATTATATGTATATTCTTTATATTTTTTCATTTACTTTATTTATTTTTATTCTATTTTTTATT
TATCTCTATATATA
Found at i:40384 original size:10 final size:10
Alignment explanation
Indices: 40348--40376 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
40338 TCCTTTACCA
40348 TTTATTTATT
1 TTTATTTATT
40358 TTTATTTATT
1 TTTATTTATT
40368 TTTATTTAT
1 TTTATTTAT
40377 CTCTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:50308 original size:105 final size:105
Alignment explanation
Indices: 50126--51004 Score: 1557
Period size: 105 Copynumber: 8.4 Consensus size: 105
50116 CAGGTTTTAC
50126 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
50191 GACGAAGGGACCGTTGGTTGTCAACAAACATCTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
50231 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAT
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
50296 GACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
50336 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAT
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
50401 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
50441 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAT
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
50506 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAA-T
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATT
* *
50546 TCAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAT
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
50611 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
50651 TTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
50716 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAA-T
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATT
*
50756 TCAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
50821 GACGAAGGGACCGCTAGTTGTCAACAAACATTTCTCCAA-T
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATT
* *
50861 TCAGAGCCAATTTCAACTTCACAACGAAGCATATTGGACTCCAAACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
50926 GACGAAGGGACCGCTGGTTGTCAAACACACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTC-AACAAACATTTCTCAATT
50967 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGA
51005 TTCAGAACAA
Statistics
Matches: 749, Mismatches: 20, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
104 3 0.00
105 690 0.92
106 56 0.07
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:52607 original size:18 final size:17
Alignment explanation
Indices: 52586--52619 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52576 CCCTATTATT
52586 ATTATATACTATATTTTC
1 ATTAT-TACTATATTTTC
*
52604 ATTATTATTATATTTT
1 ATTATTACTATATTTT
52620 ATTCCTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATTACTATATTTTC
Found at i:52654 original size:38 final size:37
Alignment explanation
Indices: 52608--52681 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
52598 ATTTTCATTA
52608 TTATTATA-TTTTATTCCTT-TATTT-ATATATATATATC
1 TTATTATATTTTTATT--TTAT-TTTAATATATATATATC
52645 TTATGTATATTTTTATTTTATTTTAATATATATATAT
1 TTAT-TATATTTTTATTTTATTTTAATATATATATAT
52682 ACACATGACC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
37 9 0.27
38 17 0.52
39 7 0.21
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (37 bp):
TTATTATATTTTTATTTTATTTTAATATATATATATC
Found at i:52798 original size:19 final size:19
Alignment explanation
Indices: 52774--52821 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
52764 TATGTATATT
52774 CTTTATATTTTTTCATTTA
1 CTTTATATTTTTTCATTTA
*
52793 CTTTAT-TTATTTTTATTTA
1 CTTTATATT-TTTTCATTTA
* *
52812 TTTTTTATTT
1 CTTTATATTT
52822 ATCTCTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.08
19 20 0.83
20 2 0.08
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (19 bp):
CTTTATATTTTTTCATTTA
Found at i:52805 original size:21 final size:18
Alignment explanation
Indices: 52779--52821 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
52769 ATATTCTTTA
52779 TATTTTTTCATTTACTTTATT
1 TATTTTTT-ATTTA-TTT-TT
52800 TA-TTTTTATTTATTTTT
1 TATTTTTTATTTATTTTT
52817 TATTT
1 TATTT
52822 ATCTCTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
19 5 0.24
20 5 0.24
21 2 0.10
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTTTTTATTTATTTTT
Found at i:52818 original size:11 final size:11
Alignment explanation
Indices: 52794--52823 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
52784 TTTCATTTAC
52794 TTTATTTA-TT
1 TTTATTTATTT
52804 TTTATTTATTT
1 TTTATTTATTT
52815 TTTATTTAT
1 TTTATTTAT
52824 CTCTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTATTTATTT
Found at i:52935 original size:143 final size:146
Alignment explanation
Indices: 52689--52957 Score: 490
Period size: 143 Copynumber: 1.9 Consensus size: 146
52679 TATACACATG
52689 ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAACATATATTTTTTTTTCT
1 ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAACA-ATATTTTTTTTTCT
*
52754 TTTATTATTCTATGTATATTCTTTATATTTTTTCATTTACTTTATTTATTTTTATT-TATTTTTT
65 TTTATTATTATATGTATATTCTTTATATTTTTTCATTTACTTTATTTATTTTTATTCTATTTTTT
52818 ATTTATCTCTATATATA
130 ATTTATCTCTATATATA
52835 ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAAC-ATA-TTTTTTTTCTT
1 ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAACAATATTTTTTTTTCTT
*
52898 TTATTATTATATGTATATTCTTTATTTTTTTTCATTTACTTTATTTATTTTTATTCTATT
66 TTATTATTATATGTATATTCTTTATATTTTTTCATTTACTTTATTTATTTTTATTCTATT
52958 GCGTTTCCTT
Statistics
Matches: 120, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
143 64 0.53
144 7 0.06
146 49 0.41
ACGTcount: A:0.26, C:0.08, G:0.04, T:0.62
Consensus pattern (146 bp):
ACCATCGTTATTTTTATTATTTTAAGTATTATTGATAGCGTATATAAACAATATTTTTTTTTCTT
TTATTATTATATGTATATTCTTTATATTTTTTCATTTACTTTATTTATTTTTATTCTATTTTTTA
TTTATCTCTATATATA
Found at i:60199 original size:27 final size:27
Alignment explanation
Indices: 60169--60236 Score: 127
Period size: 27 Copynumber: 2.5 Consensus size: 27
60159 TAAAACTACA
60169 AGTAAGAATAGTAATTAATATCATAAT
1 AGTAAGAATAGTAATTAATATCATAAT
60196 AGTAAGAATAGTAATTAATATCATAAT
1 AGTAAGAATAGTAATTAATATCATAAT
*
60223 AGTAAAAATAGTAA
1 AGTAAGAATAGTAA
60237 CAACTAGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (27 bp):
AGTAAGAATAGTAATTAATATCATAAT
Found at i:60207 original size:9 final size:9
Alignment explanation
Indices: 60169--60236 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
60159 TAAAACTACA
*
60169 AGTAAGAAT
1 AGTAATAAT
60178 AGTAATTAAT
1 AGTAA-TAAT
*
60188 A-TCATAAT
1 AGTAATAAT
*
60196 AGTAAGAAT
1 AGTAATAAT
60205 AGTAATTAAT
1 AGTAA-TAAT
*
60215 A-TCATAAT
1 AGTAATAAT
*
60223 AGTAAAAAT
1 AGTAATAAT
60232 AGTAA
1 AGTAA
60237 CAACTAGAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
8 10 0.21
9 29 0.62
10 8 0.17
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (9 bp):
AGTAATAAT
Found at i:62787 original size:2 final size:2
Alignment explanation
Indices: 62780--62805 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62770 TAGATTGGGA
62780 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
62806 GTTGAGTATT
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:77726 original size:9 final size:9
Alignment explanation
Indices: 77712--77736 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
77702 TTCGAAAAAT
77712 ATTATTTAA
1 ATTATTTAA
77721 ATTATTTAA
1 ATTATTTAA
77730 ATTATTT
1 ATTATTT
77737 TACATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
ATTATTTAA
Found at i:79159 original size:27 final size:27
Alignment explanation
Indices: 79129--79183 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
79119 ACCATAAATG
79129 AGGAAGCAAAATGGGAGGAATACACAC
1 AGGAAGCAAAATGGGAGGAATACACAC
79156 AGGAAGCAAAATGGGAGGAATACACAC
1 AGGAAGCAAAATGGGAGGAATACACAC
79183 A
1 A
79184 CATTCACATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.29, T:0.07
Consensus pattern (27 bp):
AGGAAGCAAAATGGGAGGAATACACAC
Found at i:81236 original size:20 final size:20
Alignment explanation
Indices: 81213--81250 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
81203 ATAATTATTT
81213 AAAAA-ATTAAATAAAATACC
1 AAAAATATT-AATAAAATACC
81233 AAAAATATTAATAAAATA
1 AAAAATATTAATAAAATA
81251 ATTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAATATTAATAAAATACC
Done.