Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002026.1 Hibiscus syriacus cultivar Beakdansim tig00004138_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: 66975
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4593 original size:15 final size:15
Alignment explanation
Indices: 4575--4607 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4565 AAATTCTAAA
4575 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
4590 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
4605 TAT
1 TAT
4608 ATCTGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:6299 original size:19 final size:19
Alignment explanation
Indices: 6262--6300 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6252 TCAAAGATTG
*
6262 ATTATTTTTTATTTGTAAA
1 ATTATTTTTTATATGTAAA
6281 ATTATTTTTTAATAT-TAAA
1 ATTATTTTTT-ATATGTAAA
6300 A
1 A
6301 AATATGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
ATTATTTTTTATATGTAAA
Found at i:7210 original size:16 final size:17
Alignment explanation
Indices: 7185--7218 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
7175 ATGAGGTGTC
7185 ACATTAACTTTT-CAAA
1 ACATTAACTTTTACAAA
*
7201 ACATTTACTTTTACAAA
1 ACATTAACTTTTACAAA
7218 A
1 A
7219 TAACTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (17 bp):
ACATTAACTTTTACAAA
Found at i:7882 original size:23 final size:23
Alignment explanation
Indices: 7859--7951 Score: 91
Period size: 23 Copynumber: 4.1 Consensus size: 23
7849 TGAGTGGCAT
*
7859 ATAAAATTGTCCCGAAGGACCAT
1 ATAAAATTGTCCCGAAGGACCAC
* * *
7882 AT-ATA-TGTTCCGAAAGACCAC
1 ATAAAATTGTCCCGAAGGACCAC
* *
7903 ATAGAATTGTCCCGAATGACCAC
1 ATAAAATTGTCCCGAAGGACCAC
* * *
7926 ATAGAATTATCCCTAAGGACCAC
1 ATAAAATTGTCCCGAAGGACCAC
7949 ATA
1 ATA
7952 TATGTTCCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 15 0.26
22 3 0.05
23 39 0.68
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.23
Consensus pattern (23 bp):
ATAAAATTGTCCCGAAGGACCAC
Found at i:8014 original size:21 final size:21
Alignment explanation
Indices: 7873--8032 Score: 85
Period size: 21 Copynumber: 7.4 Consensus size: 21
7863 AATTGTCCCG
*
7873 AAGGACCATATATATGTTCCGA
1 AAGGACCACATATATGTTCC-A
* * *
7895 AA-GACCACATAGAATTGTCCCG
1 AAGGACCACATA-TA-TGTTCCA
* * *
7917 AATGACCACATAGAAT-TATCCCT
1 AAGGACCACATA-TATGT-T-CCA
7940 AAGGACCACATATATGTTCCA
1 AAGGACCACATATATGTTCCA
* * *
7961 AGGGATCAAATATATG-T-CA
1 AAGGACCACATATATGTTCCA
* *
7980 TGAATGACCTCATATATGTTCCA
1 --AAGGACCACATATATGTTCCA
* * *
8003 AAGGATCACATATATGTCCCG
1 AAGGACCACATATATGTTCCA
8024 AAGGACCAC
1 AAGGACCAC
8033 GTAGAACCCT
Statistics
Matches: 105, Mismatches: 23, Indels: 21
0.70 0.15 0.14
Matches are distributed among these distances:
19 2 0.02
20 1 0.01
21 59 0.56
22 10 0.10
23 33 0.31
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:22300 original size:15 final size:15
Alignment explanation
Indices: 22276--22391 Score: 67
Period size: 15 Copynumber: 7.3 Consensus size: 15
22266 TTGAATATTC
22276 ATTT-ATATTATTAT
1 ATTTAATATTATTAT
*
22290 AATTAATATTA-TAT
1 ATTTAATATTATTAT
*
22304 TTTTAA-ATTTATTAT
1 ATTTAATA-TTATTAT
*
22319 ATTTAATATTATTTT
1 ATTTAATATTATTAT
22334 ATTATCATATATATCATTAT
1 ATT-T-A-ATAT-T-ATTAT
**
22354 ACATAATATTATTATTT
1 ATTTAATATTATTA--T
*
22371 ATTTAAATATGATTATT
1 ATTT-AATATTATTA-T
22388 ATTT
1 ATTT
22392 TATTCTAATA
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
13 1 0.01
14 13 0.16
15 27 0.34
16 3 0.04
17 14 0.18
18 14 0.18
19 2 0.03
20 5 0.06
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.58
Consensus pattern (15 bp):
ATTTAATATTATTAT
Found at i:22303 original size:20 final size:17
Alignment explanation
Indices: 22278--22321 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 17
22268 GAATATTCAT
22278 TTATATTATTATAATTAATA
1 TTATATTATTA-AATT--TA
*
22298 TTATATTTTTAAATTTA
1 TTATATTATTAAATTTA
22315 TTATATT
1 TTATATT
22322 TAATATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 9 0.39
19 4 0.17
20 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTATTAAATTTA
Found at i:22352 original size:23 final size:20
Alignment explanation
Indices: 22311--22410 Score: 55
Period size: 20 Copynumber: 5.0 Consensus size: 20
22301 TATTTTTAAA
*
22311 TTTATTATATTTAATATTAT
1 TTTATTATATATAATATTAT
*
22331 TTTATTATCATAT-ATATCAT
1 TTTATTAT-ATATAATATTAT
* * *
22351 TATA-CATA-ATATTATTA-
1 TTTATTATATATAATATTAT
* *
22368 TTTATTTAAATATGATTATTAT
1 TTTA-TTATATAT-AATATTAT
*
22390 TTTATTCTAATATTAATATTA
1 TTTATTAT-ATA-TAATATTA
22411 CCTTAGCTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
17 5 0.08
18 5 0.08
19 4 0.07
20 19 0.32
21 12 0.20
22 13 0.22
23 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (20 bp):
TTTATTATATATAATATTAT
Found at i:22393 original size:18 final size:18
Alignment explanation
Indices: 22358--22391 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
22348 CATTATACAT
*
22358 AATATTATTATTTATTTA
1 AATATGATTATTTATTTA
22376 AATATGATTA-TTATTT
1 AATATGATTATTTATTT
22392 TATTCTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
AATATGATTATTTATTTA
Found at i:25676 original size:27 final size:25
Alignment explanation
Indices: 25632--25682 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
25622 AAATCCAATA
*
25632 CGATCCAAAAAAAATAACTGAAAAC
1 CGATCCAAAAAAAATAACCGAAAAC
*
25657 CGATCCAAAAAATCGATAACCGAAAA
1 CGATCCAAAAAA--AATAACCGAAAA
25683 AAACCGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 12 0.55
27 10 0.45
ACGTcount: A:0.57, C:0.22, G:0.10, T:0.12
Consensus pattern (25 bp):
CGATCCAAAAAAAATAACCGAAAAC
Found at i:25693 original size:16 final size:17
Alignment explanation
Indices: 25663--25695 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25653 AAACCGATCC
*
25663 AAAAAATCGATAACCGA
1 AAAAAACCGATAACCGA
25680 AAAAAACCGA-AACCGA
1 AAAAAACCGATAACCGA
25696 TTTAGTGTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.21, G:0.12, T:0.06
Consensus pattern (17 bp):
AAAAAACCGATAACCGA
Found at i:26745 original size:14 final size:14
Alignment explanation
Indices: 26726--26754 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
26716 CCGATAGATT
26726 TTTCTCCTTAGGTA
1 TTTCTCCTTAGGTA
26740 TTTCTCCTTAGGTA
1 TTTCTCCTTAGGTA
26754 T
1 T
26755 AGCTTCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (14 bp):
TTTCTCCTTAGGTA
Found at i:28553 original size:22 final size:21
Alignment explanation
Indices: 28510--28553 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
28500 TACTATTATT
*
28510 ATTTTAAATTAATTTTTTCTA
1 ATTTTAAATTAATTTTTCCTA
28531 ATTTTAAAATT-ATTTTATCCTA
1 ATTTT-AAATTAATTTT-TCCTA
28553 A
1 A
28554 AATTCTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTAAATTAATTTTTCCTA
Found at i:28774 original size:35 final size:35
Alignment explanation
Indices: 28691--28774 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 35
28681 ATATTTCTAT
*
28691 ACTTTTAAATTTTATTTTTAGAGTATATAATTTAA
1 ACTTTTAAATTTTATGTTTAGAGTATATAATTTAA
*
28726 A-TTTATAAATTTTATGTTTATGA-TATGT-ATTATAA
1 ACTTT-TAAATTTTATGTTTA-GAGTATATAATT-TAA
*
28761 ACTTTTAAGTTTTA
1 ACTTTTAAATTTTA
28775 AATTTTATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
34 6 0.14
35 31 0.74
36 5 0.12
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (35 bp):
ACTTTTAAATTTTATGTTTAGAGTATATAATTTAA
Found at i:44422 original size:2 final size:2
Alignment explanation
Indices: 44415--44440 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44405 CCAATTTTTC
44415 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
44441 CTTAATGTGT
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:44587 original size:17 final size:18
Alignment explanation
Indices: 44557--44615 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
44547 TATAATTAAA
*
44557 AAATTACCAAAATAAAAT
1 AAATTACAAAAATAAAAT
*
44575 AAATTA-AAAAATAAGATT
1 AAATTACAAAAATAA-AAT
* *
44593 AATTTACAAAAAT-ATAT
1 AAATTACAAAAATAAAAT
44610 AAATTA
1 AAATTA
44616 ATAGCCCTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
17 13 0.39
18 14 0.42
19 6 0.18
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATTACAAAAATAAAAT
Found at i:45620 original size:3 final size:3
Alignment explanation
Indices: 45612--45640 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
45602 ATTTATTTTG
45612 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
45641 TGATAGTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:47195 original size:2 final size:2
Alignment explanation
Indices: 47190--47218 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47180 TGTGTGTGTG
47190 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 T
47219 TACACATCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48985 original size:27 final size:26
Alignment explanation
Indices: 48955--49032 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 26
48945 TATTTAATTT
*
48955 TTTTTAAATAATTTAGATATTTTTATA
1 TTTTTAAATAATTTA-ATAATTTTATA
*
48982 TTTTTATCAATAA-TTATTAATTTTATA
1 TTTTTA--AATAATTTAATAATTTTATA
* *
49009 TTTTTTAA-AATTTTATAATTTTAT
1 TTTTTAAATAATTTAATAATTTTAT
49033 CCTCTTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
24 2 0.05
25 13 0.30
27 20 0.47
28 3 0.07
29 5 0.12
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (26 bp):
TTTTTAAATAATTTAATAATTTTATA
Found at i:49188 original size:3 final size:3
Alignment explanation
Indices: 49180--49212 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
49170 TTATTGACCC
49180 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49213 TGGAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:49900 original size:137 final size:137
Alignment explanation
Indices: 49648--50443 Score: 932
Period size: 137 Copynumber: 5.8 Consensus size: 137
49638 AGATCCAACT
* ** * ** *
49648 GGTGTATGACATTGTTCAATCGTGATGAGGATGTCTGGCCATCTTTGAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * * *
49713 CGGTTCCTTTGTGATGAGGATGTCTGGTTATCTAAGGATGACT-CGGCTCCTACGTGATGATGAG
66 CGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGA-TGCGACTCCTTCGTGATGAGGAG
* *
49777 TTCTGGTT
130 TTCTGATC
* * ** * *
49785 AGTGGATGACATTATTCCTTTGTGATGAGGATGTCTAGACATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * * *
49850 TGGTTCCTTCGTTATGAGGACATCTGGCTATCTAAGGATGATGCTACTCCTTCGTGATGAGGAGT
66 CGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGCGACTCCTTCGTGATGAGGAGT
49915 TCTGATC
131 TCTGATC
* ** * *
49922 GGTGGATGAAATTGTTCCTTTGTGATGAAAACGTCTGGCCATCTTTATAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
* * * *
49987 CGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATGTTG-TTCCTTCGTGATGAGGAG
66 CGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATG-CGACTCCTTCGTGAT---GAG
50051 GAGTTCTGATC
127 GAGTTCTGATC
* * * * * *
50062 GGTAGATGACATTGTTCCTTCGTTATGAGGAAATTTGGCCATCTTTAAAGATATTTGAGATAAAA
1 GGTGGATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
** * ** * *
50127 CATTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATAACACGACTCCTTCATGATAAGGAGT
66 CGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGCGACTCCTTCGTGATGAGGAGT
*
50192 TCTGATT
131 TCTGATC
* * * * *
50199 GGTAGATGACATTGTTCCTTTGTGATAAGGACATCTGGCCATCTTTGAAGATATGTAAGATAACA
1 GGTGGATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
** * * * * *
50264 TAGTTCCTTCATGATGAAGACGTATGGTTATCTAAGAATG-TCGCGACTCCTTCATGATGAGGAG
66 CGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGAT-GCGACTCCTTCGTGATGAGGAG
50328 TTCTGATC
130 TTCTGATC
* * **
50336 GGTGGATGACATTGTTCATTCGTGATGAGGACATCTGATCATCTTTAAAGATATTTGAGATAACA
1 GGTGGATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
*
50401 CGGTTCCTTAGTGATGAGGACGTCTGGTTATCTAAGGATGATG
66 CGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATG
50444 TTTCCTAAAA
Statistics
Matches: 557, Mismatches: 94, Indels: 16
0.84 0.14 0.02
Matches are distributed among these distances:
136 1 0.00
137 440 0.79
138 1 0.00
139 1 0.00
140 114 0.20
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (137 bp):
GGTGGATGACATTGTTCCTTTGTGATGAGGACATCTGGCCATCTTTAAAGATATTTGAGATAACA
CGGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGCGACTCCTTCGTGATGAGGAGT
TCTGATC
Found at i:50435 original size:414 final size:414
Alignment explanation
Indices: 49653--50445 Score: 1093
Period size: 414 Copynumber: 1.9 Consensus size: 414
49643 CAACTGGTGT
** * * *
49653 ATGACATTGTTCAATCGTGATGAGGATGTCTGGCCATCTTTGAAGATATTTGAGATAACACGGTT
1 ATGACATTGTTCAATCGTGATGAGGAAATCTGGCCATCTTTAAAGATATTTGAGATAAAACAGTT
* * * * * * * * *
49718 CCTTTGTGATGAGGATGTCTGGTTATCTAAGGATGACTCGGCTCCTACGTGATGATGAGTTCTGG
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATAACACGACTCCTACATGATAAGGAGTTCTGA
* * ** * *
49783 TTAGTGGATGACATTATTCCTTTGTGATGAGGATGTCTAGACATCTTTAAAGATATTTGAGATAA
131 TTAGTAGATGACATTATTCCTTTGTGATAAGGACATCTAGACATCTTTAAAGATATGTAAGATAA
* * * * * * * *
49848 CATGGTTCCTTCGTTATGAGGACATCTGGCTATCTAAGGATGATGCTACTCCTTCGTGATGAGGA
196 CATAGTTCCTTCATGATGAAGACATATGGCTATCTAAGAATGATGCGACTCCTTCATGATGAGGA
* * * * *
49913 GTTCTGATCGGTGGATGAAATTGTTCCTTTGTGATGAAAACGTCTGGCCATCTTTATAGATATTT
261 GTTCTGATCGGTGGATGAAATTGTTCATTCGTGATGAAAACATCTGACCATCTTTAAAGATATTT
*
49978 GAGATAACACGGTTCCTTCGTGATGAGGACATCTGGCTATCTAAGGATGATGTTGTTCCTTCGTG
326 GAGATAACACGGTTCCTTAGTGATGAGGACATCTGGCTATCTAAGGATGATGTTGTTCCTTCGTG
50043 ATGAGGAGGAGTTCTGATCGGTAG
391 ATGAGGAGGAGTTCTGATCGGTAG
** * * *
50067 ATGACATTGTTCCTTCGTTATGAGGAAATTTGGCCATCTTTAAAGATATTTGAGATAAAACATTT
1 ATGACATTGTTCAATCGTGATGAGGAAATCTGGCCATCTTTAAAGATATTTGAGATAAAACAGTT
*
50132 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATAACACGACTCCTTCATGATAAGGAGTTCTGA
66 CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATAACACGACTCCTACATGATAAGGAGTTCTGA
* * * * *
50197 TTGGTAGATGACATTGTTCCTTTGTGATAAGGACATCTGGCCATCTTTGAAGATATGTAAGATAA
131 TTAGTAGATGACATTATTCCTTTGTGATAAGGACATCTAGACATCTTTAAAGATATGTAAGATAA
* *
50262 CATAGTTCCTTCATGATGAAGACGTATGGTTATCTAAGAATG-TCGCGACTCCTTCATGATGAGG
196 CATAGTTCCTTCATGATGAAGACATATGGCTATCTAAGAATGAT-GCGACTCCTTCATGATGAGG
* ** *
50326 AGTTCTGATCGGTGGATGACATTGTTCATTCGTGATGAGGACATCTGATCATCTTTAAAGATATT
260 AGTTCTGATCGGTGGATGAAATTGTTCATTCGTGATGAAAACATCTGACCATCTTTAAAGATATT
* *
50391 TGAGATAACACGGTTCCTTAGTGATGAGGACGTCTGGTTATCTAAGGATGATGTT
325 TGAGATAACACGGTTCCTTAGTGATGAGGACATCTGGCTATCTAAGGATGATGTT
50446 TCCTAAAATA
Statistics
Matches: 325, Mismatches: 53, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
413 1 0.00
414 324 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (414 bp):
ATGACATTGTTCAATCGTGATGAGGAAATCTGGCCATCTTTAAAGATATTTGAGATAAAACAGTT
CCTTCGTGATGAGGACGTCTGGTTATCTAAGGATAACACGACTCCTACATGATAAGGAGTTCTGA
TTAGTAGATGACATTATTCCTTTGTGATAAGGACATCTAGACATCTTTAAAGATATGTAAGATAA
CATAGTTCCTTCATGATGAAGACATATGGCTATCTAAGAATGATGCGACTCCTTCATGATGAGGA
GTTCTGATCGGTGGATGAAATTGTTCATTCGTGATGAAAACATCTGACCATCTTTAAAGATATTT
GAGATAACACGGTTCCTTAGTGATGAGGACATCTGGCTATCTAAGGATGATGTTGTTCCTTCGTG
ATGAGGAGGAGTTCTGATCGGTAG
Found at i:60343 original size:2 final size:2
Alignment explanation
Indices: 60336--60377 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
60326 ACCAATTTTC
60336 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
60378 CTTAATGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61387 original size:13 final size:13
Alignment explanation
Indices: 61369--61403 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
61359 GAGGCGTGGC
61369 AGCATCTGGTTGG
1 AGCATCTGGTTGG
61382 AGCATCTGGTTGG
1 AGCATCTGGTTGG
*
61395 AGCACCTGG
1 AGCATCTGG
61404 AGAAGATGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.37, T:0.26
Consensus pattern (13 bp):
AGCATCTGGTTGG
Found at i:64833 original size:17 final size:18
Alignment explanation
Indices: 64813--64846 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
64803 TTCTATAGAT
64813 ATTTAAAT-TTTTATATA
1 ATTTAAATATTTTATATA
*
64830 ATTTAGATATTTTATAT
1 ATTTAAATATTTTATAT
64847 TTTTATCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
ATTTAAATATTTTATATA
Found at i:64850 original size:26 final size:25
Alignment explanation
Indices: 64808--64877 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
64798 TCAAATTCTA
*
64808 TAGATATTTAAATTTTTAT-ATAATT
1 TAGATATTTATATTTTTATAATAA-T
64833 TAGATATTTTATATTTTTATCAATAAT
1 TAGATA-TTTATATTTTTAT-AATAAT
*
64860 TA-TTAATTTATATTTTTA
1 TAGAT-ATTTATATTTTTA
64878 AAATTTTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 6 0.15
26 25 0.64
27 4 0.10
28 4 0.10
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (25 bp):
TAGATATTTATATTTTTATAATAAT
Found at i:65048 original size:3 final size:3
Alignment explanation
Indices: 65040--65129 Score: 143
Period size: 3 Copynumber: 31.0 Consensus size: 3
65030 TTATTGACCC
65040 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
65089 ATT ATT ATT ATT -TT -TT ATT ATT ATT A-T ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
65130 TTTGAAATAA
Statistics
Matches: 83, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
2 8 0.10
3 72 0.87
4 3 0.04
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:66005 original size:88 final size:88
Alignment explanation
Indices: 65852--66014 Score: 272
Period size: 88 Copynumber: 1.9 Consensus size: 88
65842 CATTAATTAC
* * * *
65852 ACTGAAATTTCATTTAGTTAGTATAACATTTTTACTTAATTTCAATTATAAATATGAATGCAACT
1 ACTGAAATATCATTTAGTTAGCAGAACATTTTTACTTAATTTCAATTATAAATATGAATACAACT
65917 CTTTGAATATTTTGATAAATTTT
66 CTTTGAATATTTTGATAAATTTT
*
65940 ACTGAAATATCATTTAGTTAGCAGAACATTTTTACTTAATTTCAATTATAAATATGAATATAACT
1 ACTGAAATATCATTTAGTTAGCAGAACATTTTTACTTAATTTCAATTATAAATATGAATACAACT
*
66005 CTTTTAATAT
66 CTTTGAATAT
66015 AATTAAAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 69 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (88 bp):
ACTGAAATATCATTTAGTTAGCAGAACATTTTTACTTAATTTCAATTATAAATATGAATACAACT
CTTTGAATATTTTGATAAATTTT
Done.