Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009291.1 Hibiscus syriacus cultivar Beakdansim tig00112993_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: 337070
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:269896 original size:35 final size:35
Alignment explanation
Indices: 269850--269920 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 35
269840 TCGTTCAAGA
*
269850 TGGTATCGATAC-CTTCCTCAAGGTATCGGTACCCT
1 TGGTATCGATACTCTTCCTC-AGGTATCGATACCCT
* *
269885 TGGTATCGATACTGTTCTTCAGGTATCGATACCCT
1 TGGTATCGATACTCTTCCTCAGGTATCGATACCCT
269920 T
1 T
269921 TGAATGTCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 27 0.84
36 5 0.16
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (35 bp):
TGGTATCGATACTCTTCCTCAGGTATCGATACCCT
Found at i:274983 original size:21 final size:21
Alignment explanation
Indices: 274957--275001 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
274947 ACTTTGGAAT
* *
274957 TTTTCCTGGGATGCAACTAGC
1 TTTTCCTAGGACGCAACTAGC
*
274978 TTTTCCTAGGACGTAACTAGC
1 TTTTCCTAGGACGCAACTAGC
274999 TTT
1 TTT
275002 CCTTATGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.38
Consensus pattern (21 bp):
TTTTCCTAGGACGCAACTAGC
Found at i:276979 original size:27 final size:27
Alignment explanation
Indices: 276949--277004 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
276939 TCTTAAAATC
276949 AAAGAATGATGAAGTTAGGAGAGATTA
1 AAAGAATGATGAAGTTAGGAGAGATTA
276976 AAAGAATGATGAAGTTAGGAGAGATTA
1 AAAGAATGATGAAGTTAGGAGAGATTA
277003 AA
1 AA
277005 GATTAACAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (27 bp):
AAAGAATGATGAAGTTAGGAGAGATTA
Found at i:277486 original size:63 final size:64
Alignment explanation
Indices: 277375--277517 Score: 200
Period size: 64 Copynumber: 2.2 Consensus size: 64
277365 AAATTATTCA
* * *
277375 TGTGTACCGATAAACAGGAAGTGTATCAATACGCCCCTTAAAATG-AAAACATCGAATGTAATT
1 TGTGTATCGATACACAGGAAGTGTATCAATACACCCCTTAAAATGAAAAACATCGAATGTAATT
* ** *
277438 TGTGTATCGATACATAGGAAGTGTATCAATACACTTCTTGTAAA-GAAAAACATCGAATGTAATT
1 TGTGTATCGATACACAGGAAGTGTATCAATACACCCCTT-AAAATGAAAAACATCGAATGTAATT
277502 TGTGTATCGATACACA
1 TGTGTATCGATACACA
277518 CGTTAAGGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
63 34 0.49
64 36 0.51
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (64 bp):
TGTGTATCGATACACAGGAAGTGTATCAATACACCCCTTAAAATGAAAAACATCGAATGTAATT
Found at i:278139 original size:22 final size:22
Alignment explanation
Indices: 278099--278149 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
278089 AGTCGAGGGT
* *
278099 TTCATAGGTCCTTCAGGACATA
1 TTCATAGGTCCTCCAGGACAAA
*
278121 TTCATAGGTCCTCCGGGACAAA
1 TTCATAGGTCCTCCAGGACAAA
278143 TCTCATA
1 T-TCATA
278150 TGCCACTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (22 bp):
TTCATAGGTCCTCCAGGACAAA
Found at i:292835 original size:23 final size:24
Alignment explanation
Indices: 292800--292863 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
292790 TAAAGAAGAA
292800 TTTCTAT-C-CTTGTGACACAT-T
1 TTTCTATGCTCTTGTGACACATGT
* *
292821 TTTCTCTGCTCTTGTGGCACATGT
1 TTTCTATGCTCTTGTGACACATGT
292845 TTTCTATGCTCTTGTGACA
1 TTTCTATGCTCTTGTGACA
292864 TAATCTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 6 0.17
22 1 0.03
23 11 0.31
24 18 0.50
ACGTcount: A:0.14, C:0.23, G:0.16, T:0.47
Consensus pattern (24 bp):
TTTCTATGCTCTTGTGACACATGT
Found at i:293661 original size:33 final size:33
Alignment explanation
Indices: 293624--293694 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 33
293614 CCTTTACAAC
*
293624 TCCCTAGTTTTTCACA-GGATAAACTAGAACATT
1 TCCCTAGCTTTT-ACAGGGATAAACTAGAACATT
* * *
293657 TCCCTAGCTTTTACATGGGCTTAGCTAGAACATT
1 TCCCTAGCTTTTACA-GGGATAAACTAGAACATT
293691 TCCC
1 TCCC
293695 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 3 0.09
33 11 0.34
34 18 0.56
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (33 bp):
TCCCTAGCTTTTACAGGGATAAACTAGAACATT
Found at i:294172 original size:10 final size:10
Alignment explanation
Indices: 294157--294202 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
294147 GTGTTCAATT
294157 ATATTTATTA
1 ATATTTATTA
294167 ATATTTATAATA
1 ATATTTAT--TA
294179 ATATTATATT-
1 ATATT-TATTA
294189 ATATTT-TTA
1 ATATTTATTA
294198 ATATT
1 ATATT
294203 ATATAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
8 2 0.06
9 6 0.19
10 13 0.41
11 1 0.03
12 7 0.22
13 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATTTATTA
Found at i:294192 original size:22 final size:20
Alignment explanation
Indices: 294157--294206 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
294147 GTGTTCAATT
294157 ATATT-TATTAATATTTATAATA
1 ATATTATATTAATATTT-T--TA
294179 ATATTATATT-ATATTTTTA
1 ATATTATATTAATATTTTTA
294198 ATATTATAT
1 ATATTATAT
294207 AAAATAATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 11 0.41
21 1 0.04
22 11 0.41
23 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTATATTAATATTTTTA
Found at i:294274 original size:30 final size:31
Alignment explanation
Indices: 294225--294320 Score: 94
Period size: 30 Copynumber: 3.2 Consensus size: 31
294215 CAATTATATT
* * *
294225 ATAATAATATAAGATATTTTATTTTAT-TTTA
1 ATAATAATATAATAAATTTT-TTATATATTTA
294256 ATAAT-ATATAATAAATTTTTTATATATTTA
1 ATAATAATATAATAAATTTTTTATATATTTA
* *
294286 ATAATGA-ATAAT--ATTATTTATATATTTCA
1 ATAATAATATAATAAATTTTTTATATATTT-A
294315 ATAATA
1 ATAATA
294321 TTTTAGTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
28 14 0.25
29 11 0.19
30 26 0.46
31 6 0.11
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (31 bp):
ATAATAATATAATAAATTTTTTATATATTTA
Found at i:294544 original size:20 final size:20
Alignment explanation
Indices: 294519--294568 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
294509 TTTTCAGATG
294519 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
294539 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
294559 TTTTTCAGAA
1 TTTTCCAGAA
294569 TTCAAATTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:294572 original size:14 final size:15
Alignment explanation
Indices: 294551--294638 Score: 97
Period size: 15 Copynumber: 5.9 Consensus size: 15
294541 TTCCAGAAAT
*
294551 GTAATTCATTTTTCA
1 GTAATTCATTTTCCA
**
294566 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
294580 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
294595 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
***
294610 GTAATTCAAACTCCA
1 GTAATTCATTTTCCA
294625 GTAATTCATTTTCC
1 GTAATTCATTTTCC
294639 GGAAAACCAA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
14 11 0.18
15 50 0.82
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:294576 original size:20 final size:20
Alignment explanation
Indices: 294519--294577 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
294509 TTTTCAGATG
**
294519 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
**
294539 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
* *
294559 TTTTTCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
294578 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:294587 original size:15 final size:15
Alignment explanation
Indices: 294567--294632 Score: 105
Period size: 15 Copynumber: 4.4 Consensus size: 15
294557 CATTTTTCAG
294567 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
**
294582 AATTCATTTTCCAGT
1 AATTCAAATTCCAGT
294597 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
*
294612 AATTCAAACTCCAGT
1 AATTCAAATTCCAGT
294627 AATTCA
1 AATTCA
294633 TTTTCCGGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:294603 original size:30 final size:30
Alignment explanation
Indices: 294551--294632 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
294541 TTCCAGAAAT
*
294551 GTAATTCATTTTTCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
294580 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
***
294610 GTAATTCAAACTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
294633 TTTTCCGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:295752 original size:29 final size:30
Alignment explanation
Indices: 295689--295752 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
295679 CAAGATTAAA
* *
295689 ATAATTAAATTTAAGATTTATATATCTTTT
1 ATAATTAAATTTAAGATTTATATATCATTC
*
295719 A-AATTAAATTTAATA-TTATAT-TGCATTC
1 ATAATTAAATTTAAGATTTATATAT-CATTC
295747 ATAATT
1 ATAATT
295753 TAATGATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.03
28 10 0.34
29 17 0.59
30 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (30 bp):
ATAATTAAATTTAAGATTTATATATCATTC
Found at i:296677 original size:61 final size:61
Alignment explanation
Indices: 296590--296733 Score: 180
Period size: 61 Copynumber: 2.3 Consensus size: 61
296580 TGCACTAAGC
*
296590 TTACACTCTAGTGCTAATCCGAATATGATACATAAGGTCATGCCCACCACCTACACTAGGT
1 TTACACTCTAGTGCTAATCCGAATATGACACATAAGGTCATGCCCACCACCTACACTAGGT
* * * **
296651 TTACACTCTAGTGCTGATCTGGATATGACACATAAGGTTGTGCCCACCACCTACACCTAGTGT
1 TTACACTCTAGTGCTAATCCGAATATGACACATAAGGTCATGCCCACCACCTACA-CTAG-GT
* *
296714 CCTTATACACTAGTGCTAAT
1 --TTACACTCTAGTGCTAAT
296734 ATAAACCTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
61 49 0.70
62 4 0.06
63 2 0.03
65 15 0.21
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.28
Consensus pattern (61 bp):
TTACACTCTAGTGCTAATCCGAATATGACACATAAGGTCATGCCCACCACCTACACTAGGT
Found at i:297267 original size:12 final size:13
Alignment explanation
Indices: 297223--297266 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
297213 CGCCCCGATT
297223 ACCCGATTACCCG
1 ACCCGATTACCCG
*
297236 CCCCGATTACCCG
1 ACCCGATTACCCG
297249 -CCCGA-TACCCG
1 ACCCGATTACCCG
297260 ACCCGAT
1 ACCCGAT
297267 AAATATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 6 0.21
12 10 0.36
13 12 0.43
ACGTcount: A:0.20, C:0.50, G:0.16, T:0.14
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:297290 original size:2 final size:2
Alignment explanation
Indices: 297283--297377 Score: 56
Period size: 2 Copynumber: 50.0 Consensus size: 2
297273 TAAAAATAAT
* *
297283 TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA -A TA AA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * * * *
297322 -A TT TA AA TA AA AA AA TA TA TA TT TA TA TA TT TA -A TT TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
297362 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
297378 CTCGGCCCGA
Statistics
Matches: 70, Mismatches: 18, Indels: 10
0.71 0.18 0.10
Matches are distributed among these distances:
1 5 0.07
2 65 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:300310 original size:18 final size:19
Alignment explanation
Indices: 300267--300313 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
300257 TAAAATATAT
300267 TTATATTT-TAATAAAAAA
1 TTATATTTATAATAAAAAA
*
300285 TTAAATTTATGAAT-AAAAA
1 TTATATTTAT-AATAAAAAA
300304 -TATATTTATA
1 TTATATTTATA
300314 TATTTAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.04
18 15 0.60
19 6 0.24
20 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TTATATTTATAATAAAAAA
Found at i:301572 original size:31 final size:31
Alignment explanation
Indices: 301536--301599 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
301526 ATGACTGAAA
* *
301536 GACTAAAATTGAATAAATTGATAATGTTAGG
1 GACTAAAATCGAATAAATTGATAACGTTAGG
*
301567 GACTAAAATCGAATAGATTGATAACGTTAGG
1 GACTAAAATCGAATAAATTGATAACGTTAGG
301598 GA
1 GA
301600 TCATTCCCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (31 bp):
GACTAAAATCGAATAAATTGATAACGTTAGG
Found at i:301807 original size:2 final size:2
Alignment explanation
Indices: 301800--301830 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
301790 ATTTTTCTGT
301800 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
301831 GGGTTAACGT
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:307533 original size:31 final size:31
Alignment explanation
Indices: 307498--307556 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
307488 ATTACCATGA
307498 GTTCAAAGTAATAACGTGATATATATCACAT
1 GTTCAAAGTAATAACGTGATATATATCACAT
*
307529 GTTCAAAGTAATGACGTGATATATATCA
1 GTTCAAAGTAATAACGTGATATATATCA
307557 TTTGTCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (31 bp):
GTTCAAAGTAATAACGTGATATATATCACAT
Found at i:307572 original size:31 final size:31
Alignment explanation
Indices: 307501--307581 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
307491 ACCATGAGTT
* *
307501 CAAAGTAATAACGTGATATATATCACATGTT
1 CAAAGTAATGACGTGATATATATCACATGTC
**
307532 CAAAGTAATGACGTGATATATATCATTTGTC
1 CAAAGTAATGACGTGATATATATCACATGTC
* *
307563 CAAAATAATGACTTGATAT
1 CAAAGTAATGACGTGATAT
307582 TGCCACGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (31 bp):
CAAAGTAATGACGTGATATATATCACATGTC
Found at i:312719 original size:66 final size:65
Alignment explanation
Indices: 312612--312775 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 65
312602 TTTGTTGAAG
* * *
312612 GTGCATCGATGCACATGGAGTGTATCGATGCA-CTCATTTAAAATAAATGAACATCGAAT-GCCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTCA-TTAAAATAAA--AACATCGAATAG-CA
312675 -TTA
62 TTTA
* *
312678 GTGCATCGATGCATAAGGAGTGCATCGATGCACCTGC-TTAAAATACAAACATCGAATAGGATTT
1 GTGCATCGATGCATAAGGAGTGCATCGATGCACCT-CATTAAAATAAAAACATCGAATAGCATTT
312742 A
65 A
* *
312743 -TGCACCGATGCAT-GGGTAGTGCATCGATGCACC
1 GTGCATCGATGCATAAGG-AGTGCATCGATGCACC
312776 CGTCAAGGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
63 2 0.02
64 39 0.45
65 4 0.05
66 38 0.44
67 2 0.02
68 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (65 bp):
GTGCATCGATGCATAAGGAGTGCATCGATGCACCTCATTAAAATAAAAACATCGAATAGCATTTA
Found at i:313333 original size:22 final size:22
Alignment explanation
Indices: 313308--313431 Score: 203
Period size: 22 Copynumber: 5.6 Consensus size: 22
313298 GAGGGTATAT
313308 TAGTCCTTCGGGACGTATCCAG
1 TAGTCCTTCGGGACGTATCCAG
313330 TAGTCCTTCGGGACGTATCCAG
1 TAGTCCTTCGGGACGTATCCAG
* *
313352 TGGTCCTTTGGGACGTATCCAG
1 TAGTCCTTCGGGACGTATCCAG
*
313374 TAGTCCTTCAGGACGTATCCAG
1 TAGTCCTTCGGGACGTATCCAG
*
313396 TGGTCCTTCGGGACGTATCCAG
1 TAGTCCTTCGGGACGTATCCAG
*
313418 TGGTCCTTCGGGAC
1 TAGTCCTTCGGGAC
313432 AAATACTGAA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 95 1.00
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.28
Consensus pattern (22 bp):
TAGTCCTTCGGGACGTATCCAG
Found at i:319916 original size:13 final size:13
Alignment explanation
Indices: 319898--319922 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
319888 TGCAACGTGA
319898 AATAAATAAAAAG
1 AATAAATAAAAAG
319911 AATAAATAAAAA
1 AATAAATAAAAA
319923 AAACTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Found at i:322334 original size:56 final size:55
Alignment explanation
Indices: 322145--322514 Score: 507
Period size: 55 Copynumber: 6.7 Consensus size: 55
322135 TGGTTTTATC
* * **
322145 CCCTATTGCTTCAGGGAGTA-AA-ACTCGAA-AATCTTCGTCAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * * * * * *
322197 CCCCATTT-TTCCAGAGAGTAAAAGACTCAAACGAT-TCTCGATAATCATGTCTGCT
1 CCCTATTTCTT-CAGAGAGTATAAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
*
322252 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
322307 CCCTATTTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTA-TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
322363 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * *
322418 CCCTATTTTCTTTAGAGAGTATGAGACTCGAACAATCTTCAACAATCGCGTCTGCT
1 CCCTA-TTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
322474 CCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTCAA
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
322515 TTATCGTTGG
Statistics
Matches: 284, Mismatches: 25, Indels: 15
0.88 0.08 0.05
Matches are distributed among these distances:
51 2 0.01
52 14 0.05
53 2 0.01
54 7 0.02
55 150 0.53
56 109 0.38
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
Found at i:322368 original size:111 final size:111
Alignment explanation
Indices: 322145--322514 Score: 534
Period size: 111 Copynumber: 3.4 Consensus size: 111
322135 TGGTTTTATC
* * ** *
322145 CCCTATTGCTTCAGGGAGTA-AA-ACTCGAA-AATCTTCGTCAATCGTGTCTGCTCCCCATTTT-
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTTC
* ** * * * * *
322206 TCCAGAGAGTAAAAGACTCAAACGAT-TCTCGATAATCATGTCTGCT
66 TTCAGAGAGTATGAGACTCGAACAATCT-TCAACAATCGTGTCTGCT
*
322252 CCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTTC
322317 TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
66 TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
322363 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAACAATCGTGTCTGCTCCCTATTTTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTTC
* *
322428 TTTAGAGAGTATGAGACTCGAACAATCTTCAACAATCGCGTCTGCT
66 TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
*
322474 CCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTCAA
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
322515 TTATCGTTGG
Statistics
Matches: 238, Mismatches: 20, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
107 18 0.08
108 1 0.00
109 7 0.03
110 29 0.12
111 182 0.76
112 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (111 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTTC
TTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCGTGTCTGCT
Found at i:323525 original size:8 final size:8
Alignment explanation
Indices: 323512--323568 Score: 56
Period size: 8 Copynumber: 7.9 Consensus size: 8
323502 TCTTGAACCC
323512 TCATTTTT
1 TCATTTTT
323520 TCATTTTTT
1 TCA-TTTTT
323529 TCA----T
1 TCATTTTT
323533 TCATTTTT
1 TCATTTTT
323541 T-ATTTTT
1 TCATTTTT
323548 T-A-TTTT
1 TCATTTTT
323554 TCATTTTT
1 TCATTTTT
323562 TCATTTT
1 TCATTTT
323569 CACTCATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
4 4 0.10
6 5 0.12
7 9 0.21
8 16 0.38
9 8 0.19
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (8 bp):
TCATTTTT
Found at i:323536 original size:21 final size:22
Alignment explanation
Indices: 323512--323568 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
323502 TCTTGAACCC
323512 TCATTTTTTCATTTTTT-TCAT
1 TCATTTTTTCATTTTTTATCAT
**
323533 TCATTTTTT-ATTTTTTATTTT
1 TCATTTTTTCATTTTTTATCAT
323554 TCATTTTTTCATTTT
1 TCATTTTTTCATTTT
323569 CACTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 7 0.22
21 20 0.62
22 5 0.16
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (22 bp):
TCATTTTTTCATTTTTTATCAT
Found at i:323545 original size:7 final size:7
Alignment explanation
Indices: 323535--323568 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
323525 TTTTTCATTC
323535 ATTTTTT
1 ATTTTTT
323542 ATTTTTT
1 ATTTTTT
*
323549 ATTTTTC
1 ATTTTTT
323556 ATTTTTT
1 ATTTTTT
323563 CATTTT
1 -ATTTT
323569 CACTCATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:323552 original size:14 final size:15
Alignment explanation
Indices: 323512--323568 Score: 66
Period size: 14 Copynumber: 4.0 Consensus size: 15
323502 TCTTGAACCC
323512 TCATTTTTTCATTTT
1 TCATTTTTTCATTTT
**
323527 T--TTCATTCATTTT
1 TCATTTTTTCATTTT
*
323540 TTATTTTTT-ATTTT
1 TCATTTTTTCATTTT
323554 TCATTTTTTCATTTT
1 TCATTTTTTCATTTT
323569 CACTCATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 11 0.32
14 13 0.38
15 10 0.29
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (15 bp):
TCATTTTTTCATTTT
Found at i:323589 original size:42 final size:40
Alignment explanation
Indices: 323512--323594 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 40
323502 TCTTGAACCC
**
323512 TCATTTTTTCATTTTTTTCATTCATTTTTTATTTTTTATTTT
1 TCATTTTTTCATTTTACTCATT-ATTTTTTATTTTTT-TTTT
*
323554 TCATTTTTTCATTTTCACTCATT-TTTTCTTCTTTTTTTTTT
1 TCATTTTTTCATTTT-ACTCATTATTTT-TTATTTTTTTTTT
323595 CTTCAAGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 8 0.22
42 23 0.64
43 5 0.14
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (40 bp):
TCATTTTTTCATTTTACTCATTATTTTTTATTTTTTTTTT
Found at i:335211 original size:13 final size:13
Alignment explanation
Indices: 335193--335217 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
335183 TGCAACGTGA
335193 AATAAATAAAAAG
1 AATAAATAAAAAG
335206 AATAAATAAAAA
1 AATAAATAAAAA
335218 AACTATATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AATAAATAAAAAG
Done.