Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007611.1 Hibiscus syriacus cultivar Beakdansim tig00022662_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: 112837
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:2350 original size:3 final size:3
Alignment explanation
Indices: 2342--2371 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2332 GTATTAATTT
2342 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2372 TATTCTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2657 original size:12 final size:12
Alignment explanation
Indices: 2640--2673 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2630 ATATAATTTA
*
2640 TTAATTAAAATT
1 TTAATTAAAATG
2652 TTAATTAAAATG
1 TTAATTAAAATG
2664 TTAA-TAAAAT
1 TTAATTAAAAT
2674 AGTATAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
TTAATTAAAATG
Found at i:5321 original size:3 final size:3
Alignment explanation
Indices: 5313--5342 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5303 GTATTAATTT
5313 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5343 TATTCTTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5634 original size:12 final size:12
Alignment explanation
Indices: 5617--5649 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5607 TATAATTTAA
*
5617 TAATTAAAATTT
1 TAATTAAAATGT
5629 TAATTAAAATGT
1 TAATTAAAATGT
5641 TAA-TAAAAT
1 TAATTAAAAT
5650 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:6671 original size:24 final size:24
Alignment explanation
Indices: 6603--6698 Score: 115
Period size: 24 Copynumber: 4.0 Consensus size: 24
6593 CATAAATTAG
6603 GTCAAGTATCATATCAGAAAT-CAA
1 GTCAAGTATCATATCAG-AATCCAA
* *
6627 GTCAAGTAACATATCAAAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
* *
6651 GTCAAGTATCAAATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAA
*
6675 GTCATA-TATCAGATCAGAATCCAA
1 GTCA-AGTATCATATCAGAATCCAA
6699 ATCGAGAATC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 3 0.05
24 58 0.94
25 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:9240 original size:13 final size:13
Alignment explanation
Indices: 9218--9278 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
9208 CGCCGGTCAA
*
9218 CGGGTTAACGGGT
1 CGGGTCAACGGGT
*
9231 CGGGTCAACGAGT
1 CGGGTCAACGGGT
**
9244 CGGGTCGGGTCGGGT
1 CGGGTC--AACGGGT
*
9259 CGGGTCAATGGGT
1 CGGGTCAACGGGT
9272 CGGGTCA
1 CGGGTCA
9279 GGTTGTGACC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 28 0.74
15 10 0.26
ACGTcount: A:0.13, C:0.20, G:0.48, T:0.20
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:11394 original size:24 final size:24
Alignment explanation
Indices: 11367--11418 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
11357 AACGGATATA
*
11367 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
11391 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
11415 TCAA
1 TCAA
11419 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:11419 original size:24 final size:25
Alignment explanation
Indices: 11383--11484 Score: 117
Period size: 24 Copynumber: 4.3 Consensus size: 25
11373 ATCAAAACAT
11383 AAAT-CAGGTCAAGTATCATATCAG
1 AAATCCAGGTCAAGTATCATATCAG
*
11407 AAAT-CAGGTCAAGTAACATATCAG
1 AAATCCAGGTCAAGTATCATATCAG
* *
11431 -AATCCAAGTCAAGTATCAGATCAG
1 AAATCCAGGTCAAGTATCATATCAG
*
11455 -AATCCATGTC-AGATATCATATCAG
1 AAATCCAGGTCAAG-TATCATATCAG
11479 -AATCCA
1 AAATCCA
11485 AATCAAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
23 5 0.07
24 65 0.93
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (25 bp):
AAATCCAGGTCAAGTATCATATCAG
Found at i:11456 original size:48 final size:48
Alignment explanation
Indices: 11390--11499 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 48
11380 CATAAATCAG
*
11390 GTCAAGTATCATATCAGAAAT-CAGGTCA-AGTAACATATCAGAATCCAA
1 GTCAAGTATCAGATCAG-AATCCAGGTCAGA-TAACATATCAGAATCCAA
* *
11438 GTCAAGTATCAGATCAGAATCCATGTCAGATATCATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAGGTCAGATAACATATCAGAATCCAA
* **
11486 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
11500 AAAATATTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
47 3 0.06
48 50 0.93
49 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGATAACATATCAGAATCCAA
Found at i:11496 original size:24 final size:24
Alignment explanation
Indices: 11390--11496 Score: 108
Period size: 24 Copynumber: 4.5 Consensus size: 24
11380 CATAAATCAG
* *
11390 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAATATCATATCAG-AATCCAA
* *
11414 GTCAAGTAACATATCAGAATCCAA
1 GTCAAATATCATATCAGAATCCAA
* * *
11438 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAATATCATATCAGAATCCAA
*
11462 GTCAGATATCATATCAGAATCCAA
1 GTCAAATATCATATCAGAATCCAA
* *
11486 ATCAAAAATCA
1 GTCAAATATCA
11497 GATAAAATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
23 3 0.04
24 67 0.96
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (24 bp):
GTCAAATATCATATCAGAATCCAA
Found at i:13909 original size:13 final size:13
Alignment explanation
Indices: 13887--13919 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
13877 CAACGGTCAA
*
13887 CGGGTTAACGGGT
1 CGGGTCAACGGGT
13900 CGGGTCAACGGGT
1 CGGGTCAACGGGT
13913 CGGGTCA
1 CGGGTCA
13920 GGTTGTGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.21, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:16011 original size:24 final size:24
Alignment explanation
Indices: 15984--16035 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
15974 AACGGATATA
*
15984 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
16008 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
16032 TCAA
1 TCAA
16036 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:16074 original size:24 final size:24
Alignment explanation
Indices: 16007--16102 Score: 106
Period size: 24 Copynumber: 4.0 Consensus size: 24
15997 CATAAATCAG
*
16007 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCATATCAG-AATCCAA
*
16031 GTCAAGTAACATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
* * *
16055 GTCAAGTCTCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAA
*
16079 GTC-AGATATCATGTCAGAATCCAA
1 GTCAAG-TATCATATCAGAATCCAA
16103 ATCGAAAATC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 5 0.08
24 55 0.92
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:17310 original size:18 final size:18
Alignment explanation
Indices: 17289--17323 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17279 TGCCATCCGG
*
17289 TCTTATTATTTAATTTAA
1 TCTTATCATTTAATTTAA
*
17307 TCTTATCATTTACTTTA
1 TCTTATCATTTAATTTA
17324 GTCATTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTATCATTTAATTTAA
Found at i:20792 original size:24 final size:24
Alignment explanation
Indices: 20765--20816 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
20755 AACGGATATA
*
20765 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
20789 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
20813 TCAA
1 TCAA
20817 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:20817 original size:24 final size:25
Alignment explanation
Indices: 20781--20879 Score: 109
Period size: 24 Copynumber: 4.1 Consensus size: 25
20771 ATCAAAACAT
20781 AAAT-CAGGTCAAGTATCATATCAG
1 AAATCCAGGTCAAGTATCATATCAG
*
20805 AAAT-CAGGTCAAGTAACATATCAG
1 AAATCCAGGTCAAGTATCATATCAG
* * *
20829 -AATCCAAGTCAAGTCTCAGATCAG
1 AAATCCAGGTCAAGTATCATATCAG
*
20853 -AATCCATGTC-AGATATCATATCAG
1 AAATCCAGGTCAAG-TATCATATCAG
20877 AAA
1 AAA
20880 CCAAATCGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
23 5 0.08
24 57 0.89
25 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.23
Consensus pattern (25 bp):
AAATCCAGGTCAAGTATCATATCAG
Found at i:22989 original size:23 final size:23
Alignment explanation
Indices: 22960--23006 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
22950 GGTTAACGGA
22960 TCGGGTCAACAGGTCGGGTCGGG
1 TCGGGTCAACAGGTCGGGTCGGG
**
22983 TCGGGTCAAGGGGTCGGGTCGGG
1 TCGGGTCAACAGGTCGGGTCGGG
23006 T
1 T
23007 TGTGACCGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.19, G:0.51, T:0.19
Consensus pattern (23 bp):
TCGGGTCAACAGGTCGGGTCGGG
Found at i:24903 original size:2 final size:2
Alignment explanation
Indices: 24896--24924 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24886 TTTTTAAAAC
24896 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 A
24925 CCCCAATCCC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25117 original size:24 final size:24
Alignment explanation
Indices: 25090--25165 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
25080 TATATCAAAA
* *
25090 ATCAAAACATAAATCATGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
25114 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* * * *
25138 AACATATCAG-AATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAGGTCAAGT
25162 ATCA
1 ATCA
25166 GATTAGAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 3 0.07
24 41 0.93
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:25173 original size:24 final size:24
Alignment explanation
Indices: 25107--25202 Score: 97
Period size: 24 Copynumber: 4.0 Consensus size: 24
25097 CATAAATCAT
*
25107 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCATATCAG-AATCCAA
*
25131 GTCAAGTAACATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
* * *
25155 GTCAAGTATCAGATTAGAATCCAT
1 GTCAAGTATCATATCAGAATCCAA
* *
25179 GTC-AGATATCAAATCATAATCCAA
1 GTCAAG-TATCATATCAGAATCCAA
25203 ATAAAAAATC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 5 0.08
24 55 0.92
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:30006 original size:2 final size:2
Alignment explanation
Indices: 30001--30031 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29991 AAAAATATCT
30001 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 T
30032 TTCCAAGGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31298 original size:23 final size:23
Alignment explanation
Indices: 31272--31316 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31262 TGTTATAAAT
31272 ATTAAATAATTTAAT-AATAATAC
1 ATTAAATAATTT-ATGAATAATAC
**
31295 ATTATTTAATTTATGAATAATA
1 ATTAAATAATTTATGAATAATA
31317 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
ATTAAATAATTTATGAATAATAC
Found at i:31853 original size:18 final size:18
Alignment explanation
Indices: 31832--31871 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
31822 ATATATATAT
*
31832 ATATTATTTTTCTAAAAA
1 ATATTATTTTTATAAAAA
*
31850 ATATTATTTTTATAAATA
1 ATATTATTTTTATAAAAA
31868 ATAT
1 ATAT
31872 AAAATTACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATTTTTATAAAAA
Found at i:34432 original size:17 final size:17
Alignment explanation
Indices: 34383--34434 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 17
34373 TTTTAATTAC
34383 TATTGAAAATAATAATAT
1 TATT-AAAATAATAATAT
* *
34401 T-TTAAAA-ACT-TTAT
1 TATTAAAATAATAATAT
34415 TATTAAAATAATAATAT
1 TATTAAAATAATAATAT
34432 TAT
1 TAT
34435 ATAATATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 6 0.22
17 8 0.30
18 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TATTAAAATAATAATAT
Found at i:37711 original size:27 final size:29
Alignment explanation
Indices: 37667--37735 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 29
37657 ATTAAATAAT
* * *
37667 TTAATAATAATACATTTA-TG-TAATTTA
1 TTAATAATATTACATTTATTGAAAATTCA
**
37694 TTAATAATATTATTTTTATTGAAAATTCA
1 TTAATAATATTACATTTATTGAAAATTCA
37723 TTATATAATATTA
1 TTA-ATAATATTA
37736 AAATAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 15 0.44
28 2 0.06
29 8 0.24
30 9 0.26
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (29 bp):
TTAATAATATTACATTTATTGAAAATTCA
Found at i:40651 original size:65 final size:65
Alignment explanation
Indices: 40471--40680 Score: 182
Period size: 65 Copynumber: 3.2 Consensus size: 65
40461 TGTTTCAGAG
* * * * *
40471 TGATGCACCGATGCACCA-ATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCACCATA-CCATGCACCGATACACTCA-GGATTATA-TGAAACATCGAATGC
40533 ATT
63 ATT
* * * * *
40536 TCATGCATCGATGCA-TATACCTTGCACCGATGCACTGAGGATTATATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACCATACCATGCACCGATACACTCAGGATTATATG-AAACATCGAATGCAT
40600 T
65 T
* * *
40601 TGATGCATCGATGCACCA-GCCATGCATCGATACACTCTGGCTATT-T-TGAAACATCGAATGCA
1 TGATGCATCGATGCACCATACCATGCACCGATACACTCAGG--ATTATATGAAACATCGAATGCA
**
40663 CA
64 TT
40665 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
40681 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
63 2 0.02
64 51 0.43
65 62 0.52
66 2 0.02
67 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (65 bp):
TGATGCATCGATGCACCATACCATGCACCGATACACTCAGGATTATATGAAACATCGAATGCATT
Found at i:42652 original size:21 final size:21
Alignment explanation
Indices: 42628--42667 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
42618 AAAACTCTAT
42628 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
42649 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
42668 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:48393 original size:14 final size:15
Alignment explanation
Indices: 48371--48401 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
48361 TAAATTGTCA
48371 TTTCATAAATTCTAT
1 TTTCATAAATTCTAT
48386 TTTC-TAAATTCTAT
1 TTTCATAAATTCTAT
48400 TT
1 TT
48402 ATATTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTCATAAATTCTAT
Found at i:48463 original size:18 final size:19
Alignment explanation
Indices: 48433--48473 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
48423 ATATATATAT
48433 ATATTATTTTTTATGAAA-A
1 ATATTATTTTTTAT-AAATA
48452 ATATTA-TTTTTATAAATA
1 ATATTATTTTTTATAAATA
48470 ATAT
1 ATAT
48474 AAAAACTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATATTATTTTTTATAAATA
Found at i:51123 original size:27 final size:28
Alignment explanation
Indices: 51079--51146 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
51069 ATTAAACAAT
* * *
51079 TTAATAATAATACATTTA-TGTAATTTA
1 TTAATAATATTACATTTATTGAAATTCA
**
51106 TTAATAATATTATTTTTATTGAAATTCA
1 TTAATAATATTACATTTATTGAAATTCA
51134 TTATATAATATTA
1 TTA-ATAATATTA
51147 AAATAAAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 15 0.44
28 10 0.29
29 9 0.26
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (28 bp):
TTAATAATATTACATTTATTGAAATTCA
Found at i:56642 original size:37 final size:37
Alignment explanation
Indices: 56566--56642 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
56556 AAAATTATTA
**
56566 TATAATATTAAAATAAAAGTATAATATTATATATCAT
1 TATAATATTAAAATAAAAGTATAATATTATATAGAAT
* *
56603 TATAATATTAAAGAATATAA-TATCATATTAT-TAGAAT
1 TATAATATT-AA-AATAAAAGTATAATATTATATAGAAT
56640 TAT
1 TAT
56643 GAGTAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
37 16 0.47
38 12 0.35
39 6 0.18
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.42
Consensus pattern (37 bp):
TATAATATTAAAATAAAAGTATAATATTATATAGAAT
Found at i:56677 original size:12 final size:12
Alignment explanation
Indices: 56660--56692 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
56650 TATAATTTAA
*
56660 TAATTAAAATTT
1 TAATTAAAATGT
56672 TAATTAAAATGT
1 TAATTAAAATGT
56684 TAA-TAAAAT
1 TAATTAAAAT
56693 AGTATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATTAAAATGT
Found at i:60040 original size:19 final size:19
Alignment explanation
Indices: 60016--60067 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
60006 TTCTAGGTAA
60016 GGTGCATCGATGCATAAGT
1 GGTGCATCGATGCATAAGT
*
60035 GGTGCATCGGTGCATAAGT
1 GGTGCATCGATGCATAAGT
* *
60054 AGTGCGTCGATGCA
1 GGTGCATCGATGCA
60068 CACCTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.23, C:0.17, G:0.35, T:0.25
Consensus pattern (19 bp):
GGTGCATCGATGCATAAGT
Found at i:67436 original size:48 final size:48
Alignment explanation
Indices: 67380--67488 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 48
67370 AAATATTTTA
*
67380 TCTGATTTCTGA-CTTGAATTTTGTTATGATACATGACT-TGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGTTATGATACATG-CTCTGAATTCTGT
* * ** *
67428 TCTGATTTCTGATCTGGATTCTGTTCTGATATTTGTTCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGTTATGATACATGCTCTGAATTCTGT
*
67476 TTTGATTTCTGAT
1 TCTGATTTCTGAT
67489 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 1 0.02
48 50 0.96
49 1 0.02
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.51
Consensus pattern (48 bp):
TCTGATTTCTGATCTGAATTCTGTTATGATACATGCTCTGAATTCTGT
Found at i:67443 original size:12 final size:12
Alignment explanation
Indices: 67422--67486 Score: 71
Period size: 12 Copynumber: 5.4 Consensus size: 12
67412 ATGACTTGAA
67422 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
67434 TTCTGATCTGGA-
1 TTCTGTTCT-GAT
67446 TTCTGTTCTGAT
1 TTCTGTTCTGAT
*
67458 ATT-TGTTCTGAA
1 -TTCTGTTCTGAT
*
67470 TTCTGTTTTGAT
1 TTCTGTTCTGAT
67482 TTCTG
1 TTCTG
67487 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 4 0.09
12 36 0.82
13 4 0.09
ACGTcount: A:0.12, C:0.14, G:0.18, T:0.55
Consensus pattern (12 bp):
TTCTGTTCTGAT
Found at i:67448 original size:24 final size:24
Alignment explanation
Indices: 67380--67488 Score: 100
Period size: 24 Copynumber: 4.5 Consensus size: 24
67370 AAATATTTTA
*
67380 TCTGATTTCTGA-CTTGAATTTTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* *
67404 TATGA-TACATGA-CTTGAATTCTGT
1 TCTGATTTC-TGATC-TGAATTCTGT
*
67428 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
67452 TCTGATATT-TGTTCTGAATTCTGT
1 TCTGAT-TTCTGATCTGAATTCTGT
*
67476 TTTGATTTCTGAT
1 TCTGATTTCTGAT
67489 ATCTCCGTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
23 4 0.06
24 61 0.87
25 5 0.07
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.51
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:68344 original size:18 final size:18
Alignment explanation
Indices: 68317--68356 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
68307 ATATATATAT
* *
68317 ATATTTTTTTTCTAAAAA
1 ATATTATTTTTATAAAAA
*
68335 ATATTATTTTTATAAATA
1 ATATTATTTTTATAAAAA
68353 ATAT
1 ATAT
68357 AAAAGTCCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTATTTTTATAAAAA
Found at i:78592 original size:20 final size:21
Alignment explanation
Indices: 78556--78598 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
78546 AGAATATTAT
78556 ATATAATTATAATATTAAAGA
1 ATATAATTATAATATTAAAGA
* *
78577 ATATAA-TATCATATTATAGA
1 ATATAATTATAATATTAAAGA
78597 AT
1 AT
78599 TATGAGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (21 bp):
ATATAATTATAATATTAAAGA
Found at i:81965 original size:18 final size:19
Alignment explanation
Indices: 81935--81975 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
81925 ATATATATAT
81935 ATATTAGTTTTTATGAAA-A
1 ATATTAGTTTTTAT-AAATA
81954 ATATTA-TTTTTATAAATA
1 ATATTAGTTTTTATAAATA
81972 ATAT
1 ATAT
81976 AAAAGTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATATTAGTTTTTATAAATA
Found at i:82718 original size:263 final size:263
Alignment explanation
Indices: 82251--82773 Score: 1028
Period size: 263 Copynumber: 2.0 Consensus size: 263
82241 TTGAGAACAC
82251 AAAAAGCTATTGAGTTTTAACATAAAAAGCATTCCTTAGAAAAAGTTTGTGTGATTATGAATGAC
1 AAAAAGCTATTGAGTTTTAACATAAAAAGCATTCCTTAGAAAAAGTTTGTGTGATTATGAATGAC
82316 TCCTTTTAACTTAAATTTTTATTTAATAGTTTAAAATTATTTTATTAGAAATTATTTAAAAAATT
66 TCCTTTTAACTTAAATTTTTATTTAATAGTTTAAAATTATTTTATTAGAAATTATTTAAAAAATT
*
82381 AGTAATCTTTACTTTTAATAGAACTTAATTGATAAATAGTGCTTTTGAATTACGAGAGCTTCATT
131 AGTAATCTTTACTTTTAATAGAACTTAATTGATAAATAGTGCTTTTGAATTACCAGAGCTTCATT
82446 AAAAAATTGAAAATTTTGTTCATTTTTTAATTTGAATTTAAATTATGTCGCATCATATGAAGTAT
196 AAAAAATTGAAAATTTTGTTCATTTTTTAATTTGAATTTAAATTATGTCGCATCATATGAAGTAT
82511 CAT
261 CAT
82514 AAAAAGCTATTGAGTTTTAACATAAAAAGCATTCCTTAGAAAAAGTTTGTGTGATTATGAATGAC
1 AAAAAGCTATTGAGTTTTAACATAAAAAGCATTCCTTAGAAAAAGTTTGTGTGATTATGAATGAC
*
82579 TCCTTTTAACTTAAATTTTTATTTAATAGTTTAAAATTATTTTATTAGAACTTATTTAAAAAATT
66 TCCTTTTAACTTAAATTTTTATTTAATAGTTTAAAATTATTTTATTAGAAATTATTTAAAAAATT
82644 AGTAATCTTTACTTTTAATAGAACTTAATTGATAAATAGTGCTTTTGAATTACCAGAGCTTCATT
131 AGTAATCTTTACTTTTAATAGAACTTAATTGATAAATAGTGCTTTTGAATTACCAGAGCTTCATT
82709 AAAAAATTGAAAATTTTGTTCATTTTTTAATTTGAATTTAAATTATGTCGCATCATATGAAGTAT
196 AAAAAATTGAAAATTTTGTTCATTTTTTAATTTGAATTTAAATTATGTCGCATCATATGAAGTAT
82774 ATCACGTTGA
Statistics
Matches: 258, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
263 258 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (263 bp):
AAAAAGCTATTGAGTTTTAACATAAAAAGCATTCCTTAGAAAAAGTTTGTGTGATTATGAATGAC
TCCTTTTAACTTAAATTTTTATTTAATAGTTTAAAATTATTTTATTAGAAATTATTTAAAAAATT
AGTAATCTTTACTTTTAATAGAACTTAATTGATAAATAGTGCTTTTGAATTACCAGAGCTTCATT
AAAAAATTGAAAATTTTGTTCATTTTTTAATTTGAATTTAAATTATGTCGCATCATATGAAGTAT
CAT
Found at i:86152 original size:29 final size:31
Alignment explanation
Indices: 86110--86176 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
86100 TTGAAAAATC
* *
86110 ATTATATATTATTA-AA-ATAAAAGTATAAT
1 ATTATATATCATTATAATATAAAAGAATAAT
*
86139 ATTATATATCATTATAATATTAAAGAATAAT
1 ATTATATATCATTATAATATAAAAGAATAAT
*
86170 ATCATAT
1 ATTATAT
86177 TATAGAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 13 0.41
30 2 0.06
31 17 0.53
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTATATATCATTATAATATAAAAGAATAAT
Found at i:91993 original size:28 final size:29
Alignment explanation
Indices: 91961--92033 Score: 78
Period size: 31 Copynumber: 2.5 Consensus size: 29
91951 TTGAAAAATC
*
91961 ATTATATATTATTA-AATA-AAAGTATAAT
1 ATTATATATTATTATAATATAAAGAAT-AT
*
91989 ATTATATATCATTATAATATTAAAGAATAT
1 ATTATATATTATTATAATA-TAAAGAATAT
*
92019 AATATCATATTATTA
1 ATTAT-ATATTATTA
92034 GAATTTTGAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 13 0.35
29 4 0.11
30 6 0.16
31 14 0.38
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (29 bp):
ATTATATATTATTATAATATAAAGAATAT
Found at i:92489 original size:18 final size:19
Alignment explanation
Indices: 92459--92499 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
92449 ATATATATAT
92459 ATATTATTTTTTATGAAA-A
1 ATATTATTTTTTAT-AAATA
92478 ATATTA-TTTTTATAAATA
1 ATATTATTTTTTATAAATA
92496 ATAT
1 ATAT
92500 AAAAGTCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.57
19 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
ATATTATTTTTTATAAATA
Found at i:94032 original size:17 final size:18
Alignment explanation
Indices: 94010--94043 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
94000 TTAAGAGAAA
*
94010 TTAATTA-CATTTTCACT
1 TTAATTATCAGTTTCACT
94027 TTAATTATCAGTTTCAC
1 TTAATTATCAGTTTCAC
94044 ATCAATAAAA
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:0.29, C:0.18, G:0.03, T:0.50
Consensus pattern (18 bp):
TTAATTATCAGTTTCACT
Found at i:94790 original size:29 final size:30
Alignment explanation
Indices: 94757--94847 Score: 80
Period size: 31 Copynumber: 3.1 Consensus size: 30
94747 TTGAAAAGTC
94757 ATTATATATTATTA-AAATAAAAGTATAAT
1 ATTATATATTATTAGAAATAAAAGTATAAT
* * * *
94786 ATTATATATCATTATAATATTAAAGAAT-AT
1 ATTATATATTATTAGAA-ATAAAAGTATAAT
* * *
94816 AGTATCATATTATTAGAATTATAAGTA-AAT
1 ATTAT-ATATTATTAGAAATAAAAGTATAAT
94846 AT
1 AT
94848 AATTTAATAA
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
29 13 0.28
30 16 0.34
31 18 0.38
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
ATTATATATTATTAGAAATAAAAGTATAAT
Found at i:95252 original size:2 final size:2
Alignment explanation
Indices: 95245--95276 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
95235 AATTCTTGAC
95245 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
95277 TAAAGTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98400 original size:2 final size:2
Alignment explanation
Indices: 98393--98423 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
98383 TTAATTCTTG
98393 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
98424 AATTTTTAAG
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:101093 original size:27 final size:27
Alignment explanation
Indices: 101047--101106 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
101037 GAAAAATCAT
*
101047 TATAT-ATTATAAAATAAAAGTATATA
1 TATATCATTATAAAATAAAAGAATATA
* *
101073 TATATCATTATAATATTAAAGAATATA
1 TATATCATTATAAAATAAAAGAATATA
101100 -ATATCAT
1 TATATCAT
101107 ATTATTAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (27 bp):
TATATCATTATAAAATAAAAGAATATA
Found at i:101112 original size:23 final size:26
Alignment explanation
Indices: 101063--101113 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
101053 TTATAAAATA
*
101063 AAAGTATATATATATCATTATAATATT
1 AAAGAATATATATATCATTAT-ATATT
101090 AAAGAATATA-ATATCA-TAT-TATT
1 AAAGAATATATATATCATTATATATT
101113 A
1 A
101114 GAATTATGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 5 0.22
25 3 0.13
26 6 0.26
27 9 0.39
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (26 bp):
AAAGAATATATATATCATTATATATT
Found at i:104567 original size:2 final size:2
Alignment explanation
Indices: 104560--104594 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
104550 TTAATTCTTG
104560 AT AT 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 AT AT A
104595 ATTTTTTAAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:107016 original size:20 final size:21
Alignment explanation
Indices: 106980--107021 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
106970 ATTAAAATAT
*
106980 TATAAATATAGTTTTA-TAAA
1 TATAAATATAGTATTATTAAA
107000 TATAAATATAAG-ATTATTAAA
1 TATAAATAT-AGTATTATTAAA
107021 T
1 T
107022 TTTATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (21 bp):
TATAAATATAGTATTATTAAA
Found at i:107315 original size:31 final size:30
Alignment explanation
Indices: 107246--107318 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
107236 AAATCATTAT
* *
107246 ATATTATTA-AA-ATAAAAGTATATATATT
1 ATATTATTAGAATATAAAAGAATATATATC
* *
107274 ATCATCATTAGAATATTAAAGAATATAATATC
1 AT-ATTATTAGAATATAAAAGAATAT-ATATC
107306 ATATTATTAGAAT
1 ATATTATTAGAAT
107319 TATGAGTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.06
29 6 0.17
30 2 0.06
31 20 0.56
32 6 0.17
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (30 bp):
ATATTATTAGAATATAAAAGAATATATATC
Done.