Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005988.1 Hibiscus syriacus cultivar Beakdansim tig00014081_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: 54821
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:4434 original size:18 final size:19
Alignment explanation
Indices: 4399--4448 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
4389 ATATTTAATC
*
4399 AACTATATATTAATTTACT
1 AACTATATATTAACTTACT
4418 AACTATA-ATTAACTTACT
1 AACTATATATTAACTTACT
**
4436 TTCTATATATTAA
1 AACTATATATTAA
4449 ATAATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (19 bp):
AACTATATATTAACTTACT
Found at i:5199 original size:11 final size:11
Alignment explanation
Indices: 5183--5231 Score: 98
Period size: 11 Copynumber: 4.5 Consensus size: 11
5173 ATCGTGAACG
5183 ATCGACGATGA
1 ATCGACGATGA
5194 ATCGACGATGA
1 ATCGACGATGA
5205 ATCGACGATGA
1 ATCGACGATGA
5216 ATCGACGATGA
1 ATCGACGATGA
5227 ATCGA
1 ATCGA
5232 TGTTACCCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (11 bp):
ATCGACGATGA
Found at i:6668 original size:89 final size:90
Alignment explanation
Indices: 6490--6669 Score: 283
Period size: 90 Copynumber: 2.0 Consensus size: 90
6480 TGTTAAACTA
6490 GCTACCGGTTTGTTTAAAGGTACAATAATAATGTAAACGGTAAAATATTTCAACTTAACCAGTAA
1 GCTACCGGTTTGTTTAAAGGTACAATAATAATGTAAACGGTAAAATATTTCAACTTAACCAGTAA
* *
6555 AAATAAAATAGACGCATCCTATTAC
66 AAATAAAATAGACACAGCCTATTAC
* * *
6580 GCTACCGGTTTGTTTAAAGGTATAAT-ATAATGTAAACGGTAAAATATTTACAACTTAACCTGTT
1 GCTACCGGTTTGTTTAAAGGTACAATAATAATGTAAACGGTAAAATATTT-CAACTTAACCAGTA
*
6644 AAAAT-AAATAGGCACAGCCTATTAC
65 AAAATAAAATAGACACAGCCTATTAC
6669 G
1 G
6670 TTAAACTAGC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 41 0.49
90 42 0.51
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (90 bp):
GCTACCGGTTTGTTTAAAGGTACAATAATAATGTAAACGGTAAAATATTTCAACTTAACCAGTAA
AAATAAAATAGACACAGCCTATTAC
Found at i:6739 original size:72 final size:73
Alignment explanation
Indices: 6663--6868 Score: 292
Period size: 72 Copynumber: 2.8 Consensus size: 73
6653 AGGCACAGCC
* *
6663 TATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAATAATGT-AACGATAAAAAATAT
1 TATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAAAATAG
*
6727 GTGCAACT
66 GTGCAACA
* * * *
6735 TATTACGTTAAACTAACTACTGGTTTGTTTAAAGGT-TAATAATAATGTAAATGGTAAAATAAAA
1 TATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAA-CG-ATAA-AAAA
6799 TAGGTGCAACA
63 TAGGTGCAACA
*
6810 TA-TACGTTAAACTAGCTACCGGTATGTTTAAAGGTATAATAATAATGTAAACGATAAAA
1 TATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAA
6869 TATTTACAAC
Statistics
Matches: 117, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
71 12 0.10
72 37 0.32
73 4 0.03
74 34 0.29
75 30 0.26
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (73 bp):
TATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAAAATAG
GTGCAACA
Found at i:6822 original size:74 final size:75
Alignment explanation
Indices: 6663--6870 Score: 282
Period size: 75 Copynumber: 2.8 Consensus size: 75
6653 AGGCACAGCC
* * *
6663 TATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAATAATGT-AACG-ATAA-AAAAT
1 TATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAAGGTAAAATAAAAT
* *
6725 ATGTGCAACT
66 AGGTGCAACA
* *
6735 TATTACGTTAAACTAACTACTGGTTTGTTTAAAGGT-TAATAATAATGTAAATGGTAAAATAAAA
1 TATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAA-GGTAAAATAAAA
6799 TAGGTGCAACA
65 TAGGTGCAACA
* *
6810 TA-TACGTTAAACTAGCTACCGGTATGTTTAAAGGTATAATAATAATGTAAACGATAAAATA
1 TATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAA-GGTAAAATA
6871 TTTACAACTT
Statistics
Matches: 119, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
71 12 0.10
72 35 0.29
73 1 0.01
74 33 0.28
75 38 0.32
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (75 bp):
TATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAAGGTAAAATAAAAT
AGGTGCAACA
Found at i:6925 original size:100 final size:99
Alignment explanation
Indices: 6789--6970 Score: 292
Period size: 100 Copynumber: 1.8 Consensus size: 99
6779 ATGTAAATGG
** *
6789 TAAAATAAAATAGGTGCAACATATACGTTAAACTAGCTACCGGTATGTTTAAAGGTATAATAATA
1 TAAAATAAAATAGGCACAACATATACGTTAAACTAGCTACCAGTATGTTTAAAGGTATAATAATA
6854 ATGTAAACGATAAAATATTTACAACTTAATTGGT
66 ATGTAAACGATAAAATATTTACAACTTAATTGGT
* * * *
6888 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTTTTTAAAGGTATAATACT
1 TAAAATAAAATAGGCACAACATA-TACGTTAAACTAGCTACCAGTATGTTTAAAGGTATAATAAT
6953 AATGTAAACGATAAAATA
65 AATGTAAACGATAAAATA
6971 AAATAGGTGC
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
99 20 0.27
100 55 0.73
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.31
Consensus pattern (99 bp):
TAAAATAAAATAGGCACAACATATACGTTAAACTAGCTACCAGTATGTTTAAAGGTATAATAATA
ATGTAAACGATAAAATATTTACAACTTAATTGGT
Found at i:6971 original size:175 final size:174
Alignment explanation
Indices: 6730--7045 Score: 463
Period size: 175 Copynumber: 1.8 Consensus size: 174
6720 AAAATATGTG
* ** * *
6730 CAACTTATTACGTTAAACTAACTACTGGTTTGTTTAAAGGTTAATAATAATGTAAATGGTAAAAT
1 CAACCTATTACGTTAAACTAACTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGATAAAAT
* *
6795 AAAATAGGTGCAACATA-TACGTTAAACTAGCTACCGGTATGTTTAAAGGTATAATAATAATGTA
66 AAAATAGGTGCAACATATTACGTTAAACTAACTACCAGTATGTTTAAA-GTATAATAATAATGTA
6859 AACGATAAAATATTTACAACTTAATTGGTTAAAATAAAATAGGCA
130 AACGATAAAATATTTACAACTTAATTGGTTAAAATAAAATAGGCA
* * *
6904 CAACCTATTACGTTAAACTAGCTACCAGTTTTTTTAAAGGTATAATACTAATGTAAACGATAAAA
1 CAACCTATTACGTTAAACTAACTACCAGTTTGTTTAAAGGT-TAATAATAATGTAAACGATAAAA
* * * * *
6969 TAAAATAGGTGCAACTTATTAGGTTAAACTAACTACTAGTTTGTTTAAAGTTTAATAATAATGTA
65 TAAAATAGGTGCAACATATTACGTTAAACTAACTACCAGTATGTTTAAAGTATAATAATAATGTA
*
7034 AACGGTAAAATA
130 AACGATAAAATA
7046 AAATAGGCAC
Statistics
Matches: 124, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
174 36 0.29
175 63 0.51
176 25 0.20
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (174 bp):
CAACCTATTACGTTAAACTAACTACCAGTTTGTTTAAAGGTTAATAATAATGTAAACGATAAAAT
AAAATAGGTGCAACATATTACGTTAAACTAACTACCAGTATGTTTAAAGTATAATAATAATGTAA
ACGATAAAATATTTACAACTTAATTGGTTAAAATAAAATAGGCA
Found at i:7034 original size:250 final size:251
Alignment explanation
Indices: 6580--7219 Score: 1021
Period size: 250 Copynumber: 2.6 Consensus size: 251
6570 ATCCTATTAC
* *
6580 GCTACCGGTTTGTTTAAAGGTATAAT-ATAATGTAAACGGTAAAATATTTACAACTTAACCT-GT
1 GCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAATATTTACAACTTAA-TTGGT
*
6643 TAAAAT-AAATAGGCACAGCCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAAT
65 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAAT
* *
6707 AATGT-AACGAT--AA-AAAATATGTGCAACTTATTACGTTAAACTAACTACTGGTTTGTTTAAA
130 AATGTAAACGATAAAATAAAATAGGTGCAACTTATTACGTTAAACTAACTACTAGTTTGTTTAAA
* **
6768 GGTTAATAATAATGTAAATGGTAAAATAAAATAGGTGCAACATA-TACGTTAAACTA
195 GGTTAATAATAATGTAAACGGTAAAATAAAATAGGCACAACATATTACGTTAAACTA
*
6824 GCTACCGGTATGTTTAAAGGTATAATAATAATGTAAACGATAAAATATTTACAACTTAATTGGTT
1 GCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAATATTTACAACTTAATTGGTT
* *
6889 AAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTTTTTAAAGGTATAATACTA
66 AAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAATA
*
6954 ATGTAAACGATAAAATAAAATAGGTGCAACTTATTAGGTTAAACTAACTACTAGTTTGTTTAAAG
131 ATGTAAACGATAAAATAAAATAGGTGCAACTTATTACGTTAAACTAACTACTAGTTTGTTTAAAG
* *
7019 TTTAATAATAATGTAAACGGTAAAATAAAATAGGCACAACCTATTACGTTAAACTA
196 GTTAATAATAATGTAAACGGTAAAATAAAATAGGCACAACATATTACGTTAAACTA
*
7075 GCTACCGGTTTGTTTAAAGGTATAATAATAATGAAAACGATAAAATATTTACAACTTAATTGGTT
1 GCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAATATTTACAACTTAATTGGTT
* * * *
7140 -AAATAAAATAGGCACATCCTATTACATT-AACTAGCTATCAGTTTGTTTAAAGATATAATAATA
66 AAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAATA
*
7203 ATGTAAACGGTAAAATA
131 ATGTAAACGATAAAATA
7220 TTTACAGTTT
Statistics
Matches: 365, Mismatches: 23, Indels: 11
0.91 0.06 0.03
Matches are distributed among these distances:
244 26 0.07
245 39 0.11
246 60 0.16
247 6 0.02
249 49 0.13
250 110 0.30
251 75 0.21
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (251 bp):
GCTACCGGTTTGTTTAAAGGTATAATAATAATGTAAACGATAAAATATTTACAACTTAATTGGTT
AAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAATA
ATGTAAACGATAAAATAAAATAGGTGCAACTTATTACGTTAAACTAACTACTAGTTTGTTTAAAG
GTTAATAATAATGTAAACGGTAAAATAAAATAGGCACAACATATTACGTTAAACTA
Found at i:7064 original size:75 final size:76
Alignment explanation
Indices: 6888--7121 Score: 353
Period size: 76 Copynumber: 3.1 Consensus size: 76
6878 CTTAATTGGT
* *
6888 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTTTTTAAAGGTATAATACT
1 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAAT
6953 AATGTAAACGA
66 AATGTAAACGA
** * * * * *
6964 TAAAATAAAATAGGTGCAACTTATTAGGTTAAACTAACTACTAGTTTGTTTAAA-GTTTAATAAT
1 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAAT
*
7028 AATGTAAACGG
66 AATGTAAACGA
*
7039 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAAT
1 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAAT
*
7104 AATGAAAACGA
66 AATGTAAACGA
7115 TAAAATA
1 TAAAATA
7122 TTTACAACTT
Statistics
Matches: 137, Mismatches: 20, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
75 65 0.47
76 72 0.53
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (76 bp):
TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTATAATAAT
AATGTAAACGA
Found at i:7303 original size:100 final size:100
Alignment explanation
Indices: 7039--7332 Score: 439
Period size: 98 Copynumber: 3.0 Consensus size: 100
7029 ATGTAAACGG
* *
7039 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTATAATAAT
1 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGATATAATAAT
* * * *
7104 AATGAAAACGATAAAATATTTACAACTTAATTGGT
66 AATGTAAACGGTAAAATATTTACAACTTAACTAGT
* * *
7139 T-AAATAAAATAGGCACATCCTATTACATT-AACTAGCTATCAGTTTGTTTAAAGATATAATAAT
1 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGATATAATAAT
**
7202 AATGTAAACGGTAAAATATTTACAGTTTAACTAGT
66 AATGTAAACGGTAAAATATTTACAACTTAACTAGT
* * *
7237 TAAAATAAAATAGGCGCAACCTATTACGTTAAACTAGCTAGCAGTTTGTTTAATGATATAATAAT
1 TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGATATAATAAT
*
7302 AATGTAAATGGTAAAATATTTACAACTTAAC
66 AATGTAAACGGTAAAATATTTACAACTTAAC
7333 CATTTGAAAT
Statistics
Matches: 173, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
98 61 0.35
99 51 0.29
100 61 0.35
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (100 bp):
TAAAATAAAATAGGCACAACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGATATAATAAT
AATGTAAACGGTAAAATATTTACAACTTAACTAGT
Found at i:10843 original size:3 final size:3
Alignment explanation
Indices: 10835--10923 Score: 151
Period size: 3 Copynumber: 29.7 Consensus size: 3
10825 ATAGCATTTC
10835 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* **
10883 ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT AAC ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
10924 CAATCATATC
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:11242 original size:30 final size:30
Alignment explanation
Indices: 11208--11268 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
11198 GTCCCGAATG
*
11208 ACCTATCCATATGCCCCGAAGGACATAGGT
1 ACCTATCCATATACCCCGAAGGACATAGGT
*
11238 ACCTATCCATATATCCCGAAGGACATAGGT
1 ACCTATCCATATACCCCGAAGGACATAGGT
11268 A
1 A
11269 ACCCTCGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (30 bp):
ACCTATCCATATACCCCGAAGGACATAGGT
Found at i:16410 original size:30 final size:30
Alignment explanation
Indices: 16369--16429 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
16359 ATCCCAAAGG
16369 ACCTATCCATATGTTCCT-AAGGACATAGGT
1 ACCTATCCATATG-TCCTGAAGGACATAGGT
*
16399 ACCTGTCCATATGTCCTGAAGGACATAGGT
1 ACCTATCCATATGTCCTGAAGGACATAGGT
16429 A
1 A
16430 ACCCTCGACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (30 bp):
ACCTATCCATATGTCCTGAAGGACATAGGT
Found at i:27296 original size:26 final size:26
Alignment explanation
Indices: 27262--27316 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
27252 TTTGAAAATA
27262 TTTTTGAAAACATATAATATATAGTT
1 TTTTTGAAAACATATAATATATAGTT
*
27288 TTTTTGAAAGCATATAATATATAGTT
1 TTTTTGAAAACATATAATATATAGTT
27314 TTT
1 TTT
27317 AAAAATCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (26 bp):
TTTTTGAAAACATATAATATATAGTT
Found at i:27377 original size:74 final size:75
Alignment explanation
Indices: 27288--27472 Score: 209
Period size: 74 Copynumber: 2.5 Consensus size: 75
27278 ATATATAGTT
* * * * *
27288 TTTTTGAAAGCATATAATATATAGTTTTTAAAA-ATCAATTTTTGAAATATAT-ATA-ATATGGT
1 TTTTTGAAAACATATAATATATAGTTTTGAAAACA-CAATTTTTAAAACATATAATATATATAGT
27350 TTTGAAAATACG-
65 TTT-AAAA-ACGA
* *
27362 TTTTTGAAAACATATATTATATAGTTTTGAAAACACATTTTTTAAAACATATAATATATATAGTT
1 TTTTTGAAAACATATAATATATAGTTTTGAAAACACAATTTTTAAAACATATAATATATATAGTT
27427 TTAAAAACGA
66 TTAAAAACGA
* *
27437 TTTTTGAAAAACGTA-CATAATATAGTTTTGAAAACA
1 TTTTTG-AAAACATATAAT-ATATAGTTTTGAAAACA
27473 TATATTTAGT
Statistics
Matches: 95, Mismatches: 10, Indels: 10
0.83 0.09 0.09
Matches are distributed among these distances:
74 47 0.49
75 15 0.16
76 33 0.35
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (75 bp):
TTTTTGAAAACATATAATATATAGTTTTGAAAACACAATTTTTAAAACATATAATATATATAGTT
TTAAAAACGA
Found at i:27448 original size:39 final size:37
Alignment explanation
Indices: 27288--27471 Score: 175
Period size: 37 Copynumber: 4.9 Consensus size: 37
27278 ATATATAGTT
* *
27288 TTTTTGAAAGCATATA-ATATATAGTTTTTAAAAATCAA
1 TTTTTGAAAACATATATATATATAG-TTTTAAAAA-CGA
* *
27326 TTTTTG-AAATATATATA-ATATGGTTTTGAAAATACG-
1 TTTTTGAAAACATATATATATATAGTTTT-AAAA-ACGA
27362 TTTTTGAAAACATATAT-TATATAGTTTTGAAAACAC-A
1 TTTTTGAAAACATATATATATATAGTTTT-AAAA-ACGA
*
27399 TTTTTTAAAACATATAATATATATAGTTTTAAAAACGA
1 TTTTTGAAAACATAT-ATATATATAGTTTTAAAAACGA
* * *
27437 TTTTTGAAAAACGTACATA-ATATAGTTTTGAAAAC
1 TTTTTG-AAAACATATATATATATAGTTTTAAAAAC
27472 ATATATTTAG
Statistics
Matches: 124, Mismatches: 12, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
36 10 0.08
37 73 0.59
38 23 0.19
39 18 0.15
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.41
Consensus pattern (37 bp):
TTTTTGAAAACATATATATATATAGTTTTAAAAACGA
Found at i:27530 original size:26 final size:25
Alignment explanation
Indices: 27496--27551 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
27486 TAAAACGAAT
27496 TTTTTGGAAACATATATAATATATAA
1 TTTTTGGAAACATAT-TAATATATAA
* *
27522 TTTTTGGAAACATATTATTATATAG
1 TTTTTGGAAACATATTAATATATAA
27547 TTTTT
1 TTTTT
27552 ATTATATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.50
Consensus pattern (25 bp):
TTTTTGGAAACATATTAATATATAA
Found at i:27554 original size:17 final size:16
Alignment explanation
Indices: 27534--27645 Score: 88
Period size: 17 Copynumber: 6.8 Consensus size: 16
27524 TTTGGAAACA
27534 TATTATTATATAGTTTT
1 TATTATTATATA-TTTT
*
27551 TATTATATATTAAATTATAT
1 TATTAT-TA-TATATT-T-T
* *
27571 TAATATTATTTATTTT
1 TATTATTATATATTTT
27587 TATTTATTATATATTTT
1 TA-TTATTATATATTTT
*
27604 TATTTATTATATATTTA
1 TA-TTATTATATATTTT
*
27621 TATTA-TAT-TATTAT
1 TATTATTATATATTTT
27635 T-TTATTA-ATAT
1 TATTATTATATAT
27646 GTTAATTGAT
Statistics
Matches: 79, Mismatches: 9, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
13 3 0.04
14 10 0.13
15 3 0.04
16 6 0.08
17 37 0.47
18 8 0.10
19 6 0.08
20 6 0.08
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (16 bp):
TATTATTATATATTTT
Found at i:27571 original size:10 final size:11
Alignment explanation
Indices: 27556--27645 Score: 54
Period size: 10 Copynumber: 9.0 Consensus size: 11
27546 GTTTTTATTA
27556 TATATTAA-AT
1 TATATTAATAT
27566 TATATTAATAT
1 TATATTAATAT
27577 TAT-TT-AT-T
1 TATATTAATAT
*
27585 TTTATT--TAT
1 TATATTAATAT
* *
27594 TATA-TATTTT
1 TATATTAATAT
*
27604 TAT-TTATTA-
1 TATATTAATAT
*
27613 TATATTTATAT
1 TATATTAATAT
*
27624 TATATTATTAT
1 TATATTAATAT
*
27635 TTTATTAATAT
1 TATATTAATAT
27646 GTTAATTGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
8 5 0.08
9 11 0.18
10 23 0.37
11 23 0.37
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTAATAT
Found at i:27583 original size:30 final size:30
Alignment explanation
Indices: 27549--27635 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
27539 TTATATAGTT
* *
27549 TTTATTATATATTAAATTATATTAATATTA
1 TTTATTATATATTATATTATATTATTATTA
* *
27579 TTTATT-TTTATT-TATTATA-TATTTTTA
1 TTTATTATATATTATATTATATTATTATTA
27606 TTTATTATATATTTATATTATATTATTATT
1 TTTATTATATA-TTATATTATATTATTATT
27636 TTATTAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 12 0.26
28 9 0.19
29 7 0.15
30 13 0.28
31 6 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
TTTATTATATATTATATTATATTATTATTA
Found at i:27597 original size:28 final size:28
Alignment explanation
Indices: 27564--27637 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 28
27554 TATATATTAA
*
27564 ATTATATTAATATTATTTATTTTTATTT
1 ATTATATTAATATTATTTATTTTTATAT
* * *
27592 ATTATA-TATTTTTATTTA-TTATATAT
1 ATTATATTAATATTATTTATTTTTATAT
27618 -TTATATT-ATATTA-TTATTTT
1 ATTATATTAATATTATTTATTTT
27638 ATTAATATGT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
24 3 0.08
25 11 0.30
26 7 0.19
27 10 0.27
28 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (28 bp):
ATTATATTAATATTATTTATTTTTATAT
Found at i:28554 original size:19 final size:19
Alignment explanation
Indices: 28530--28585 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
28520 GAACGTTGGA
28530 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
28549 AACCGGTTTTGAACCGGTTTT
1 AACCGGTTTTG-ACCGG-TTT
*
28570 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
28586 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 9 0.26
21 8 0.24
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:28565 original size:11 final size:11
Alignment explanation
Indices: 28530--28578 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
28520 GAACGTTGGA
28530 AACCGGTTTTG
1 AACCGGTTTTG
28541 -ACCGG-TTT-
1 AACCGGTTTTG
28549 AACCGGTTTTG
1 AACCGGTTTTG
28560 AACCGGTTTTG
1 AACCGGTTTTG
28571 -ACCGGTTT
1 AACCGGTTT
28579 GACCGGTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.23
10 16 0.46
11 11 0.31
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:28581 original size:9 final size:10
Alignment explanation
Indices: 28531--28585 Score: 78
Period size: 9 Copynumber: 5.6 Consensus size: 10
28521 AACGTTGGAA
28531 ACCGGTTTTG
1 ACCGGTTTTG
*
28541 ACCGG-TTTA
1 ACCGGTTTTG
28550 ACCGGTTTTG
1 ACCGGTTTTG
28560 AACCGGTTTTG
1 -ACCGGTTTTG
28571 ACCGG-TTTG
1 ACCGGTTTTG
28580 ACCGGT
1 ACCGGT
28586 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
9 17 0.43
10 13 0.32
11 10 0.25
ACGTcount: A:0.15, C:0.22, G:0.29, T:0.35
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:28616 original size:13 final size:13
Alignment explanation
Indices: 28598--28652 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
28588 CGACCCGTTT
*
28598 ACCCGTTTACCCG
1 ACCCGTTGACCCG
28611 ACCCGTTGACCCGACCCG
1 ACCCGTTGA--C---CCG
28629 ACCCGTTGACCCG
1 ACCCGTTGACCCG
28642 ACCCGTTGACC
1 ACCCGTTGACC
28653 GTTGACCGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 22 0.61
15 1 0.03
16 1 0.03
18 12 0.33
ACGTcount: A:0.16, C:0.47, G:0.20, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:28629 original size:18 final size:18
Alignment explanation
Indices: 28606--28646 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
28596 TTACCCGTTT
28606 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
28624 ACCCGACCCGTTGACCCG
1 ACCCGACCCGTTGACCCG
28642 ACCCG
1 ACCCG
28647 TTGACCGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.51, G:0.22, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:28720 original size:29 final size:29
Alignment explanation
Indices: 28660--28725 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
28650 ACCGTTGACC
*** *
28660 GTGCTATTCTGGGAATTAATTCGGTTTTG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
28689 GTGCTATTCTGGGAATTAATTCGAAATGG
1 GTGCTATTCTGGGAATTAATTCGAAATGG
28718 GTGCTATT
1 GTGCTATT
28726 TCGGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.41
Consensus pattern (29 bp):
GTGCTATTCTGGGAATTAATTCGAAATGG
Found at i:35324 original size:25 final size:23
Alignment explanation
Indices: 35288--35346 Score: 55
Period size: 24 Copynumber: 2.4 Consensus size: 23
35278 TATTTATTTA
* * *
35288 TTTTAATTTTAACATATTCTTCAT
1 TTTTTATTTTAA-ATATTATACAT
*
35312 TTTTTATTATTAAATTTTATACAT
1 TTTTTATT-TTAAATATTATACAT
35336 TTTTTACTTTT
1 TTTTTA-TTTT
35347 TTATTTCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 23 0.79
25 6 0.21
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTTTATTTTAAATATTATACAT
Found at i:35347 original size:32 final size:30
Alignment explanation
Indices: 35273--35370 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 30
35263 TATCCTTTAA
35273 ATTTTTA-TTTATTTATTTTAATTTTAACAT
1 ATTTTTACTTT-TTTATTTTAATTTTAACAT
*
35303 ATTCTT-CATTTTTTATTATTAAATTTTATACAT
1 ATTTTTAC-TTTTTTATT-TT-AATTTTA-ACAT
*
35336 -TTTTTACTTTTTTATTTCT-CTTTTAACAT
1 ATTTTTACTTTTTTATTT-TAATTTTAACAT
35365 -TTTTTA
1 ATTTTTA
35371 TATTTATTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
29 10 0.17
30 16 0.28
31 6 0.10
32 21 0.36
33 5 0.09
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (30 bp):
ATTTTTACTTTTTTATTTTAATTTTAACAT
Found at i:35389 original size:10 final size:10
Alignment explanation
Indices: 35368--35398 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
35358 TTAACATTTT
35368 TTATATTT-A
1 TTATATTTCA
35377 TTATATTTCA
1 TTATATTTCA
35387 TTATATTTCA
1 TTATATTTCA
35397 TT
1 TT
35399 TCCTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATATTTCA
Found at i:35485 original size:37 final size:38
Alignment explanation
Indices: 35407--35492 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 38
35397 TTTCCTTTAA
35407 AATTTAA-ATTTTTGTTTATTTTATTTTATTTTTCTCT
1 AATTTAACATTTTTGTTTATTTTATTTTATTTTTCTCT
*
35444 --TTTAACATTTTT-TTACTATTTTTTTTTA-TTTTCT-T
1 AATTTAACATTTTTGTT--TATTTTATTTTATTTTTCTCT
*
35479 AATTTAACCTTTTT
1 AATTTAACATTTTT
35493 CCCCTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
35 8 0.19
36 12 0.29
37 22 0.52
ACGTcount: A:0.21, C:0.08, G:0.01, T:0.70
Consensus pattern (38 bp):
AATTTAACATTTTTGTTTATTTTATTTTATTTTTCTCT
Found at i:36579 original size:30 final size:30
Alignment explanation
Indices: 36544--36608 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
36534 TTGTGGAAGA
*
36544 GTGTGGAATCCTCTGGAATATTCTGGAGAT
1 GTGTGGAATCCTCTAGAATATTCTGGAGAT
36574 GTGTGGAATCCTCTAGAATATTCTGGAGAT
1 GTGTGGAATCCTCTAGAATATTCTGGAGAT
36604 GTGTG
1 GTGTG
36609 AACCTTATAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.34
Consensus pattern (30 bp):
GTGTGGAATCCTCTAGAATATTCTGGAGAT
Found at i:37399 original size:12 final size:12
Alignment explanation
Indices: 37382--37425 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
37372 TTAAATTTTC
37382 GTTTTATTTACT
1 GTTTTATTTACT
37394 GTTTTATTTA-T
1 GTTTTATTTACT
**
37405 AATTTATTTACT
1 GTTTTATTTACT
*
37417 TTTTTATTT
1 GTTTTATTT
37426 CATTACATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (12 bp):
GTTTTATTTACT
Found at i:38528 original size:139 final size:139
Alignment explanation
Indices: 38201--38537 Score: 353
Period size: 139 Copynumber: 2.4 Consensus size: 139
38191 ATTATTCGAT
* * *
38201 TCAATAATTCG-TTAAAATG-GACTA-GATTAATAATTAGAGTCTCCACTTTAGGCTTAATTTCA
1 TCAATAATT-GATTAAAATGAG-TTAGGATTAAT-ATTAGAGCCTCCATTTTAGGCTTAATTTCA
* * * *
38263 GTTTACTCATTTAATTTAGGAGAATTTTTTATTTGGTCCTCGTTTTTATGCTTGAGGTTCCATTT
63 CTATAATCATTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTTATGCTTGAGGTTCCATTT
*
38328 TGACCATTAGAT
128 TGACCATTAGAC
* * * * * **
38340 TCAATAATTGGTTAAAATTAGTTAGG-CTAACGT-TTAGAGCTTCCGTTTTAGTTTTAATTTCAC
1 TCAATAATTGATTAAAATGAGTTAGGATTAA--TATTAGAGCCTCCATTTTAGGCTTAATTTCAC
* *
38403 TATAATCCTTTAATTTAGGGGAATTTTTTATTTGGTCCTCGCTTTTATGCTTGAGGTTCCATTTT
64 TATAATCATTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTTATGCTTGAGGTTCCATTTT
** *
38468 GATTATTTGAC
129 GACCATTAGAC
* * * *
38479 TCAATAGTTTATTAAAAGTGA-TTTGGATTAATATTAGAGCCTACATTTTAAGGCTTAAT
1 TCAATAATTGATTAAAA-TGAGTTAGGATTAATATTAGAGCCTCCATTTT-AGGCTTAAT
38538 CTCCTAGGTT
Statistics
Matches: 159, Mismatches: 30, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
138 2 0.01
139 142 0.89
140 14 0.09
141 1 0.01
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (139 bp):
TCAATAATTGATTAAAATGAGTTAGGATTAATATTAGAGCCTCCATTTTAGGCTTAATTTCACTA
TAATCATTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTTATGCTTGAGGTTCCATTTTGA
CCATTAGAC
Found at i:43875 original size:114 final size:114
Alignment explanation
Indices: 43751--43985 Score: 389
Period size: 114 Copynumber: 2.1 Consensus size: 114
43741 TAAATTATTG
* * *
43751 AAACAAAATATAAATACATAATTAATAAAAGAAATTGAATTCTTAATTTCTTTTCTAGGACAAAT
1 AAACAAAATATAAAAACATAATTAATAAAAGAAATTGAATTCCTAAGTTCTTTTCTAGGACAAAT
* * *
43816 GAGTGGTGCATATGTATTAGTAAGGATAAAAGTATAAATTGGTTTCTAA
66 GAGTGGAGCATATGCATTAGTAAGGATAAAAATATAAATTGGTTTCTAA
* *
43865 AAGCAAAATATAAAAACATAATTAATAAAAGAAATTGAATTCCTAAGTTCTTTTCTAGGATAAAT
1 AAACAAAATATAAAAACATAATTAATAAAAGAAATTGAATTCCTAAGTTCTTTTCTAGGACAAAT
*
43930 GAGTGGAGCCTATGCATTAGTAAGGATAAAAATATAAATTGGTTTCTAA
66 GAGTGGAGCATATGCATTAGTAAGGATAAAAATATAAATTGGTTTCTAA
43979 AAACAAA
1 AAACAAA
43986 GTTGGAAATG
Statistics
Matches: 111, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 111 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.31
Consensus pattern (114 bp):
AAACAAAATATAAAAACATAATTAATAAAAGAAATTGAATTCCTAAGTTCTTTTCTAGGACAAAT
GAGTGGAGCATATGCATTAGTAAGGATAAAAATATAAATTGGTTTCTAA
Done.