Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009524.1 Hibiscus syriacus cultivar Beakdansim tig00115805_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: 72181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:3773 original size:31 final size:32
Alignment explanation
Indices: 3735--3811 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
3725 AGAATGACCT
3735 GAACCCGAATTGAATC-GA-AAATATGATACCC
1 GAACCCGAATTGAATCTGACAAATATGA-ACCC
* * **
3766 GAACCCGAACTGCATCTGACTGATATGAACCC
1 GAACCCGAATTGAATCTGACAAATATGAACCC
3798 GAACCCGAGATTGA
1 GAACCCGA-ATTGA
3812 CCTAGTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
31 14 0.38
32 14 0.38
33 9 0.24
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.18
Consensus pattern (32 bp):
GAACCCGAATTGAATCTGACAAATATGAACCC
Found at i:3868 original size:16 final size:16
Alignment explanation
Indices: 3847--3890 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
3837 AATTGTTTTC
3847 AACCTGACCTGTGATG
1 AACCTGACCTGTGATG
** *
3863 AACCTGACCTGTTTTT
1 AACCTGACCTGTGATG
3879 AACCTGACCTGT
1 AACCTGACCTGT
3891 AAATGATCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (16 bp):
AACCTGACCTGTGATG
Found at i:3931 original size:16 final size:16
Alignment explanation
Indices: 3920--3957 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
3910 TGACCTGATC
3920 TGATATTTACCTGACT
1 TGATATTTACCTGACT
3936 TGATATTTACCTGACT
1 TGATATTTACCTGACT
3952 T-ATATT
1 TGATATT
3958 ACCATGGACG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.47
Consensus pattern (16 bp):
TGATATTTACCTGACT
Found at i:4122 original size:20 final size:21
Alignment explanation
Indices: 4092--4131 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
4082 AAATAGACCT
4092 ATTATATAAAATTATTTAAAA
1 ATTATATAAAATTATTTAAAA
4113 ATTA-ATAAAATTATTTAAA
1 ATTATATAAAATTATTTAAA
4132 TGTAAATTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTATATAAAATTATTTAAAA
Found at i:4777 original size:20 final size:19
Alignment explanation
Indices: 4740--4786 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
4730 TAGTAGTACA
4740 TGCATATTA--ATTTCATT
1 TGCATATTAGTATTTCATT
*
4757 TGCATAATTAGTATTTTATT
1 TGCAT-ATTAGTATTTCATT
4777 TGCATATTAG
1 TGCATATTAG
4787 GTTAATTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 5 0.19
20 12 0.46
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (19 bp):
TGCATATTAGTATTTCATT
Found at i:5059 original size:15 final size:15
Alignment explanation
Indices: 5039--5075 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
5029 TAATTTACTT
5039 TATATAGTTTATATA
1 TATATAGTTTATATA
5054 TATATAGTTTATATA
1 TATATAGTTTATATA
5069 TACTATA
1 TA-TATA
5076 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:5114 original size:524 final size:520
Alignment explanation
Indices: 4091--5075 Score: 1405
Period size: 524 Copynumber: 1.9 Consensus size: 520
4081 TAAATAGACC
* *
4091 TATTATATAAAATTATTTAAAAATTAATAAAATTATTTAAATGTAAATTAGATAAAACATGATTG
1 TATTATATAAAATTATTTAAAAATTAATAAAATTATTTAAATGTAAAATAGATAAAACATGATTA
*
4156 ATTAGGTGTTAAATAATTAGTGTCACATTGCATATATATGGTTCATAAATAGTGGTACATGTAAT
66 ATTAGGTGTTAAATAATTAGTGTCACATTGCATATATATGGTTCA-AAATAGTAGTACATGTAAT
* * *
4221 ATTAATTTTATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAACCTAT
130 ATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATATTAGGTTAATTCACATTAATAACCCAT
4286 TTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTAGTGCTAG
195 TTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTAGTGCTAG
* *
4351 TCCATTTACATTAGTTTACATAGGCCCAATACATAAGTCCACTCTTTTATTACAAATATATATGC
260 TCCATTTACATTAGTTTACATAGACCCAATACATAAGCCCACTCTTTTATTACAAATATATATGC
*
4416 ATTAGTGCTAGTCATTTACATTAGGGGTTTGTGATTTAGGGTTTAATATTTAGATTTTATAGTTT
325 ATTAGTGCTAGTCATTTACATTAGGGGTTTGTGATTTAAGGTTTAATATTTAGATTTTATAGTTT
** * * * * *
4481 AGGGTTTAGAGTTTCTATAAACTATATAATTTATATTTTATATAGTTTATGCATAGTATTTCTAT
390 AAAGTTCAGAGTTTCTAT-AACTATATAATTTATACTTTATATAGTTTATACATAATATTTATAT
** * * *
4546 AAACTATATCAGTAATTTACTTTATATAGTTTATATATATATATACTATACATGGTTTATACATA
454 AAACTATATCAGTAATTTACTACATACAGTCTATATACATATATACTATACATGGTTTATACATA
4611 CA
519 CA
* *
4613 TATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAAATATATAAAATATGAT
1 TATTATATAAAATTATTT-A-AAAATTAATAAAATTATTTAAATGTAAAATAGATAAAACATGAT
4678 TAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTC-AAATAGTAGTACATG
64 TAATTAGGTGTTAAATAATTAG--TGTCACATTGCATA-TATATGGTTCAAAATAGTAGTACATG
* * *
4742 -CATATTAATTTCATTTGCATAATTAGTATTTTATTTGCATATTAGGTTAATTCACATTAATAGC
126 TAATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATATTAGGTTAATTCACATTAATAAC
* * * * **
4806 CCATTTATTTTGTTGTTATGAATAAGTAGTAATGAAACCCAAAATTAAGTTTATTTGCATTAGTG
191 CCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTAGTG
* * *
4871 TTAGTTCATTTACATTAGTTTACATATACCCAATACATAAGCCCACTCTTTTATTACAAATATAT
256 CTAGTCCATTTACATTAGTTTACATAGACCCAATACATAAGCCCACTCTTTTATTACAAATATAT
* *
4936 ATGCATTAGTGCTAGTCCATTTATATTA-GGGTTTGTGATTTAAGGTTTAATGTTTAG-TGTTTA
321 ATGCATTAGTGCTAGT-CATTTACATTAGGGGTTTGTGATTTAAGGTTTAATATTTAGAT-TTTA
* * *
4999 T-GATTTAAAGTTCAGGGTTTGTGAT-A-TA-AGTAA-TT-TACTTTATATAGTTTATATATATA
384 TAG-TTTAAAGTTCAGAGTTTCT-ATAACTATA-TAATTTATACTTTATATAGTTTATACATA-A
*
5058 TAGTTTATATATACTATA
445 TA-TTTATATAAACTATA
5076 CATGGTTTAT
Statistics
Matches: 415, Mismatches: 36, Indels: 24
0.87 0.08 0.05
Matches are distributed among these distances:
520 19 0.05
521 5 0.01
522 36 0.09
523 4 0.01
524 301 0.73
525 26 0.06
526 14 0.03
527 10 0.02
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (520 bp):
TATTATATAAAATTATTTAAAAATTAATAAAATTATTTAAATGTAAAATAGATAAAACATGATTA
ATTAGGTGTTAAATAATTAGTGTCACATTGCATATATATGGTTCAAAATAGTAGTACATGTAATA
TTAATTTCATTTGCATAATTAGTATTTTAGTTGCATATTAGGTTAATTCACATTAATAACCCATT
TATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGTCCATTTGCATTAGTGCTAGT
CCATTTACATTAGTTTACATAGACCCAATACATAAGCCCACTCTTTTATTACAAATATATATGCA
TTAGTGCTAGTCATTTACATTAGGGGTTTGTGATTTAAGGTTTAATATTTAGATTTTATAGTTTA
AAGTTCAGAGTTTCTATAACTATATAATTTATACTTTATATAGTTTATACATAATATTTATATAA
ACTATATCAGTAATTTACTACATACAGTCTATATACATATATACTATACATGGTTTATACATACA
Found at i:5627 original size:19 final size:19
Alignment explanation
Indices: 5587--5657 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
5577 AAATTTTCTA
**
5587 TTCCCTCTAAATTTTTCAAT
1 TTCCCTCTAAA-TTCACAAT
5607 TTCCCTCTAAATTCACAAT
1 TTCCCTCTAAATTCACAAT
* * * *
5626 TTCCATAT-ATTCTCAAAAT
1 TTCCCTCTAAAT-TCACAAT
5645 TTCCCTCTAAATT
1 TTCCCTCTAAATT
5658 TGCCAATTCC
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
18 2 0.05
19 25 0.62
20 13 0.32
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCCCTCTAAATTCACAAT
Found at i:5721 original size:2 final size:2
Alignment explanation
Indices: 5716--5951 Score: 85
Period size: 2 Copynumber: 122.5 Consensus size: 2
5706 TTAAACTCAT
* * *
5716 TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TT TA 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
* * * *
5757 T- TA CT- TA AA T- TT TT TA TA -A TT 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 TA TA TA TA TA TA
* * * * * *
5795 TA -A TA TA AA T- TA TA GTT TA TA AA CTA TA TA -A TT TT TA TA GTT
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA -TA
*
5837 TA TA TA TA TA TA TA TA TA TA GT- TCA CA TA TA TA GT- TCA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA -TA T-A TA TA
* * * *
5879 AA CA TA -A TT TA TA TA TA TA TG T- TA TA -A TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
5916 GTT TA TA -A TA TA AA TA T- 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 TA TA TA T
5952 TAGTTGTTTT
Statistics
Matches: 174, Mismatches: 33, Indels: 54
0.67 0.13 0.21
Matches are distributed among these distances:
1 18 0.10
2 148 0.85
3 8 0.05
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5896 original size:49 final size:49
Alignment explanation
Indices: 5836--5956 Score: 128
Period size: 47 Copynumber: 2.5 Consensus size: 49
5826 TTTTTATAGT
5836 TTATATATATATATATATATAGTTCACA-TATATAGTTCAT-ATA-AACATAA
1 TTATATATATATATATATATAGTT-A-ATTATATAGTTCATAATATAA-AT-A
* * *
5886 TT-TATATATATATGT-TATA-ATAATTATATAGTTTATAATATAAATA
1 TTATATATATATATATATATAGTTAATTATATAGTTCATAATATAAATA
5932 TTATATATATATATATATATTAGTT
1 TTATATATATATATATATA-TAGTT
5957 GTTTTAATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
45 1 0.02
46 15 0.25
47 18 0.31
48 8 0.14
49 14 0.24
50 3 0.05
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (49 bp):
TTATATATATATATATATATAGTTAATTATATAGTTCATAATATAAATA
Found at i:6027 original size:2 final size:2
Alignment explanation
Indices: 6016--6045 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6006 ATAATATTTT
6016 TA TA -A 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
6046 TAGTTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6040 original size:94 final size:96
Alignment explanation
Indices: 5917--6110 Score: 347
Period size: 94 Copynumber: 2.0 Consensus size: 96
5907 AATTATATAG
*
5917 TTTATAATATAAATATTATATATATATATATATATTAGTTGTTTTAATTTTTTTCTTAACTTTTG
1 TTTATAATAT-AATATTATATATATATATATATATTAGTTGTTTTAATTTTTTTCTCAACTTTTG
*
5982 AAATGAATGCAATTTTTTCATTTTATAATATT
65 AAATGAATGCAAATTTTTCATTTTATAATATT
6014 TTTATAATAT-ATA-TATATATATATATATATATTAGTTGTTTTAATTTTTTTCTCAACTTTTGA
1 TTTATAATATAATATTATATATATATATATATATTAGTTGTTTTAATTTTTTTCTCAACTTTTGA
6077 AATGAATGCAAATTTTTCATTTTATAATATT
66 AATGAATGCAAATTTTTCATTTTATAATATT
6108 TTT
1 TTT
6111 CATATTTGAT
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
94 82 0.86
95 3 0.03
97 10 0.11
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (96 bp):
TTTATAATATAATATTATATATATATATATATATTAGTTGTTTTAATTTTTTTCTCAACTTTTGA
AATGAATGCAAATTTTTCATTTTATAATATT
Found at i:6504 original size:215 final size:214
Alignment explanation
Indices: 6133--6820 Score: 1161
Period size: 215 Copynumber: 3.2 Consensus size: 214
6123 CTTCGTATTG
* * *
6133 TTTAATTTACTTAAATTTTTATTTATAATTTCATATTTTTTCAATTTAGTCCTCCAAATTTTATT
1 TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATT
*
6198 TGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGCCCCATAACTTTTTAA
66 TGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTTTAA
* *
6263 ATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAGTTATTTCGATTTGA
131 ATGGGTAT-ATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTAGATTTGA
*
6328 TCCCTCATCAATGTGTGTTC
195 TCCCTCATCAATGTGTGTTA
*
6348 TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAATTTTTATT
1 TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATT
* *
6413 TGCATCTGAAATTGACCCATACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAA
66 TGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTTTAA
*
6478 ATGGGTATACTTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTTGATTTGA
131 ATGGGTATA-TTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTAGATTTGA
*
6543 TCCATCATCAATGTGTGTTA
195 TCCCTCATCAATGTGTGTTA
* *
6563 TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTATTCAATTTAGACCTCCAAATTTTATT
1 TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATT
6628 TGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTTTAA
66 TGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTTTAA
*
6693 A----TA-ATTTAGTACTTTTTTGTATTAATTTCAACCTCACAGTTTAAAATTATTTAGATTTGA
131 ATGGGTATATTTAGTAC-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTAGATTTGA
*
6753 TCCCTCATCAATGTGTGTTG
195 TCCCTCATCAATGTGTGTTA
*
6773 TTTAATTTATTTAAATTTTTATTTGTAATTCCATATTTGTTCAATTTA
1 TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
6821 ATTCTTAAAT
Statistics
Matches: 449, Mismatches: 22, Indels: 9
0.94 0.05 0.02
Matches are distributed among these distances:
209 8 0.02
210 110 0.24
211 2 0.00
214 1 0.00
215 328 0.73
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (214 bp):
TTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATT
TGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTTTAA
ATGGGTATATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTAGATTTGAT
CCCTCATCAATGTGTGTTA
Found at i:13324 original size:9 final size:8
Alignment explanation
Indices: 13300--13398 Score: 74
Period size: 8 Copynumber: 11.9 Consensus size: 8
13290 ACACAGGGAG
13300 AAAGAAAA
1 AAAGAAAA
* *
13308 AAATAGAA
1 AAAGAAAA
* *
13316 AAA-CAAG
1 AAAGAAAA
13323 AAAGAAAA
1 AAAGAAAA
* *
13331 AAATAAAT
1 AAAGAAAA
13339 AAAGAAAA
1 AAAGAAAA
13347 AACAGAAAA
1 AA-AGAAAA
13356 AAGAGAAAA
1 AA-AGAAAA
*
13365 AGAGAAAAA
1 AAAG-AAAA
13374 AAAGAAAGA
1 AAAGAAA-A
*
13383 AAGGAGAAA
1 AAAGA-AAA
13392 AAAGAAA
1 AAAGAAA
13399 GAAGAAAGAA
Statistics
Matches: 70, Mismatches: 16, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
7 4 0.06
8 32 0.46
9 32 0.46
10 2 0.03
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (8 bp):
AAAGAAAA
Found at i:13362 original size:18 final size:18
Alignment explanation
Indices: 13341--13396 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
13331 AAATAAATAA
*
13341 AGAAAAAACAGAAAAAAG
1 AGAAAAAAGAGAAAAAAG
*
13359 AG-AAAAAGAGAAAAAAA
1 AGAAAAAAGAGAAAAAAG
13376 AGAAAGAAAGGAGAAAAAAG
1 AGAAA-AAA-GAGAAAAAAG
13396 A
1 A
13397 AAGAAGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 3 0.09
20 10 0.31
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (18 bp):
AGAAAAAAGAGAAAAAAG
Found at i:13397 original size:14 final size:14
Alignment explanation
Indices: 13298--13405 Score: 66
Period size: 14 Copynumber: 7.9 Consensus size: 14
13288 TAACACAGGG
13298 AGAAAGAA-AAAAA
1 AGAAAGAAGAAAAA
* *
13311 TAGAAA-AACAAGAA
1 -AGAAAGAAGAAAAA
*
13325 AGAAA-AA-AATAA
1 AGAAAGAAGAAAAA
* *
13337 ATAAAGAA-AAAAC
1 AGAAAGAAGAAAAA
*
13350 AGAAAAAAGAGAAAA
1 AGAAAGAAGA-AAAA
*
13365 AGAGAA-AAAAAAGAA
1 AGA-AAGAAGAAA-AA
*
13380 AGAAAGGAGAAAAA
1 AGAAAGAAGAAAAA
13394 AGAAAGAAGAAA
1 AGAAAGAAGAAA
13406 GAAAACCAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
12 8 0.11
13 20 0.27
14 27 0.36
15 18 0.24
16 2 0.03
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.03
Consensus pattern (14 bp):
AGAAAGAAGAAAAA
Found at i:13397 original size:18 final size:19
Alignment explanation
Indices: 13350--13410 Score: 74
Period size: 18 Copynumber: 3.3 Consensus size: 19
13340 AAGAAAAAAC
13350 AGAAAAAAGAGAA-AAAGAG
1 AGAAAAAAGA-AAGAAAGAG
*
13369 AAAAAAAAGAAAGAAAG-G
1 AGAAAAAAGAAAGAAAGAG
*
13387 AGAAAAAAGAAAG-AAGAA
1 AGAAAAAAGAAAGAAAGAG
13405 AGAAAA
1 AGAAAA
13411 CCAATCAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.08
18 21 0.57
19 13 0.35
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (19 bp):
AGAAAAAAGAAAGAAAGAG
Found at i:13410 original size:17 final size:16
Alignment explanation
Indices: 13314--13410 Score: 60
Period size: 16 Copynumber: 6.1 Consensus size: 16
13304 AAAAAAATAG
*
13314 AAAAACAAGAAAGAAA
1 AAAAAGAAGAAAGAAA
*
13330 AAAATA-AATAAAGAAA
1 AAAA-AGAAGAAAGAAA
* * *
13346 AAACAGAAAAAAG-AG
1 AAAAAGAAGAAAGAAA
13361 AAAAAG-AGAAA-AAA
1 AAAAAGAAGAAAGAAA
13375 AAGAAAGAAAGGAGAA-AAA
1 AA-AAAG-AA-GA-AAGAAA
*
13394 AGAAAGAAGAAAGAAA
1 AAAAAGAAGAAAGAAA
13410 A
1 A
13411 CCAATCAAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
14 7 0.11
15 13 0.20
16 28 0.44
17 4 0.06
18 6 0.09
19 6 0.09
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAAGAAGAAAGAAA
Found at i:14072 original size:27 final size:28
Alignment explanation
Indices: 14034--14092 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
14024 CAAAGAATCC
* *
14034 AACCTGAAACACATTACC-TCCC-AGATT
1 AACCCGAAACACATGACCTTCCCAAG-TT
14061 AACCCGAAACACATGACCTTCCCAAGTT
1 AACCCGAAACACATGACCTTCCCAAGTT
14089 AACC
1 AACC
14093 TAAGCCTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 16 0.57
28 10 0.36
29 2 0.07
ACGTcount: A:0.37, C:0.36, G:0.08, T:0.19
Consensus pattern (28 bp):
AACCCGAAACACATGACCTTCCCAAGTT
Found at i:14834 original size:171 final size:172
Alignment explanation
Indices: 14548--14887 Score: 560
Period size: 171 Copynumber: 2.0 Consensus size: 172
14538 TTGATCACTT
*
14548 TTTAAGTCTTAATTTGGTTATGGCATCGTGAAGAGAAGCCCTATGTCAATTCGATAACATTGCTG
1 TTTAAGTCTTAATTTGGTTATGGCATCGTGAAGAGAAGCCCTATGTCAATTCGATAACATTACTG
* *
14613 ATTAGTGACACTAGAGTGAAACAATTCGAGATTAAGATTTTGTCATGAAGAGAGCCATGAGTACC
66 ATTAGTGACACCAGAGTGAAACAATTCGAGATTAAGATTTTGGCATGAAGAGAGCCATGAGTACC
14678 CACATTGGGG-ATTACCTAAACCAGATGTCATTAAGATCACGA
131 CACATTGGGGCATTACCTAAACCAGATGTC-TTAAGATCACGA
* * *
14720 TTTAAGTGTTCATTTGGTTATGGCATCGTGAAGAGAAGCCCT-TAGTCTATT-GATAACATTACT
1 TTTAAGTCTTAATTTGGTTATGGCATCGTGAAGAGAAGCCCTAT-GTCAATTCGATAACATTACT
* *
14783 GATTAGTGACACCAGAGTGAAACTATTCGAGATTAAGATTTTGGCATGAAGAGAGCCTTGAGTAC
65 GATTAGTGACACCAGAGTGAAACAATTCGAGATTAAGATTTTGGCATGAAGAGAGCCATGAGTAC
*
14848 CCACATTGGGGCATTATCTAAACCAGATGTCTTAAGATCA
130 CCACATTGGGGCATTACCTAAACCAGATGTCTTAAGATCA
14888 TGAGATTTAA
Statistics
Matches: 157, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
171 93 0.59
172 64 0.41
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (172 bp):
TTTAAGTCTTAATTTGGTTATGGCATCGTGAAGAGAAGCCCTATGTCAATTCGATAACATTACTG
ATTAGTGACACCAGAGTGAAACAATTCGAGATTAAGATTTTGGCATGAAGAGAGCCATGAGTACC
CACATTGGGGCATTACCTAAACCAGATGTCTTAAGATCACGA
Found at i:15678 original size:42 final size:42
Alignment explanation
Indices: 15618--15701 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
15608 AAGGTTTTCT
* *
15618 TGATGATTAAGTCATTCGGGCCATCAATAAGTCTTTCGAGCA
1 TGATGATTAAATCATTCGGGCCATCAATAAGTCTTTCAAGCA
* * * **
15660 TGATGCTTAAATCCTTCGGGTCATTTATAAGTCTTTCAAGCA
1 TGATGATTAAATCATTCGGGCCATCAATAAGTCTTTCAAGCA
15702 AGAAGATAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (42 bp):
TGATGATTAAATCATTCGGGCCATCAATAAGTCTTTCAAGCA
Found at i:16216 original size:42 final size:41
Alignment explanation
Indices: 16170--16289 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 41
16160 AACAGTTTCT
16170 TGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
1 TGATGAGTAAGTCCTTCGGGCCATCA-TAAGTCTTTCGAGCA
* * * * *
16212 TGATGCGTAAGTCCTTTGAGCCATTTATAAGTCTTTCGAGTA
1 TGATGAGTAAGTCCTTCGGGCCA-TCATAAGTCTTTCGAGCA
* *
16254 GGATGA-TAAGTCCTTCGGGCCATCCATAAGACTTTC
1 TGATGAGTAAGTCCTTCGGGCCAT-CATAAGTCTTTC
16290 AGGTAGGATT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
40 1 0.02
41 24 0.37
42 38 0.58
43 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (41 bp):
TGATGAGTAAGTCCTTCGGGCCATCATAAGTCTTTCGAGCA
Found at i:16474 original size:261 final size:261
Alignment explanation
Indices: 15877--16621 Score: 1046
Period size: 261 Copynumber: 2.8 Consensus size: 261
15867 AATTTTTATG
* * * *
15877 AGAAACTAAGCTTGATTTTCATGGTTTTATTAATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
1 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
* * ** *
15942 TCGAGCATGATGCTTAAGTCCTTCGGGATATTTATAAGTCTTTCGAGCTAAATGATAAGACCTTC
66 TCGAGCATGATGCGTAAGTCCTTTGGGCCATTTATAAGTCTTTCGAG-TAGATGATAAGACCTTC
* * * * *
16007 GAGCCATCCATAAGACCTTCGGACAAGATGTTTTCAACATTTTTCGTGCTCGATTAATCACATAT
130 GGGCCATCCATAAGACATTCGG-CAAGATGTTTTCAACATTTCTGGTACTCGATTAATCACATAT
* * *
16072 GGAGTTGAATAAATAACACCTCACTCGAAGGACCAACATAATATGTAGGGGTTCCTTGATGACAA
194 GGAGTTGAATCAACAACACCTCACTCGAAGGACCAACATAATATATAGGGGTTCCTTGATGACAA
*
16137 TTA
259 CTA
** *
16140 AGAAACTAAGCTTGATTTTCAACAGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTT
1 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
* *
16205 TCGAGCATGATGCGTAAGTCCTTTGAGCCATTTATAAGTCTTTCGAGTAGGATGATAAGTCCTTC
66 TCGAGCATGATGCGTAAGTCCTTTGGGCCATTTATAAGTCTTTCGAGTA-GATGATAAGACCTTC
* * * *
16270 GGGCCATCCATAAGACTTTCAGGTAGGATTTTTTCAACATTTCTGGTACTCGATTAATCACATAT
130 GGGCCATCCATAAGACATTC-GGCAAGATGTTTTCAACATTTCTGGTACTCGATTAATCACATAT
* * *
16335 GGAG-T-AATCAGCAATACCTCACTCGAGGGACCAACATAATATATAGGGGTTCCTTGATGACAA
194 GGAGTTGAATCAACAACACCTCACTCGAAGGACCAACATAATATATAGGGGTTCCTTGATGACAA
16398 CTA
259 CTA
16401 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
1 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
* * * * *
16466 TTGAGCATGATGCGTAAGT-CTTTCGGGCCATTTATAACTTTTTAGAGCAAGATGATAAGACCTT
66 TCGAGCATGATGCGTAAGTCCTTT-GGGCCATTTATAAGTCTTTCGAG-TAGATGATAAGACCTT
* * * *
16530 CGGGCTATCCATAAGACATTCGGGCAAAATGTTTTCAAAATTTCTGGTACTTGATTAATCACATA
129 CGGGCCATCCATAAGACATTC-GGCAAGATGTTTTCAACATTTCTGGTACTCGATTAATCACATA
*
16595 TAGAGTTGAATCAACAACACCTCACTC
193 TGGAGTTGAATCAACAACACCTCACTC
16622 TAGGAATCAA
Statistics
Matches: 425, Mismatches: 51, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
260 4 0.01
261 226 0.53
262 5 0.01
263 188 0.44
264 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (261 bp):
AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGGGCCATCAGTAAGTCTT
TCGAGCATGATGCGTAAGTCCTTTGGGCCATTTATAAGTCTTTCGAGTAGATGATAAGACCTTCG
GGCCATCCATAAGACATTCGGCAAGATGTTTTCAACATTTCTGGTACTCGATTAATCACATATGG
AGTTGAATCAACAACACCTCACTCGAAGGACCAACATAATATATAGGGGTTCCTTGATGACAACT
A
Found at i:18396 original size:21 final size:21
Alignment explanation
Indices: 18358--18406 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
18348 TAGGTCCTCA
*
18358 TATTTTATGTTTATTTTAATT
1 TATTTTATGTTTACTTTAATT
*
18379 TATTTTATGTTGT-CTTTATTT
1 TATTTTATGTT-TACTTTAATT
*
18400 TACTTTA
1 TATTTTA
18407 CTTTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.69
Consensus pattern (21 bp):
TATTTTATGTTTACTTTAATT
Found at i:18422 original size:5 final size:5
Alignment explanation
Indices: 18358--18415 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
18348 TAGGTCCTCA
* * * * *
18358 TATTT TATGTT TATTT TAATT TATTT TATGT TGTCTT TATTT TACTT TACTT
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TAT-TT TATTT TATTT TATTT
18410 TATTT T
1 TATTT T
18416 TTATTTTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 35 0.81
6 8 0.19
ACGTcount: A:0.19, C:0.05, G:0.05, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:20101 original size:39 final size:39
Alignment explanation
Indices: 20047--20125 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
20037 TCAAAGCTAC
20047 AAGTTTAGACTATTCTATGACTAAATCGTGCTTGTTTTA
1 AAGTTTAGACTATTCTATGACTAAATCGTGCTTGTTTTA
20086 AAGTTTAGACTATTCTATGACTAAATCGTGCTTGTTTTA
1 AAGTTTAGACTATTCTATGACTAAATCGTGCTTGTTTTA
20125 A
1 A
20126 GTTAAAATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (39 bp):
AAGTTTAGACTATTCTATGACTAAATCGTGCTTGTTTTA
Found at i:26178 original size:6 final size:5
Alignment explanation
Indices: 26139--26182 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
26129 TAGGCCCTCA
* *
26139 TATTT TATGTT TATTT TAATT TATTT TATGT TATCTT TATTT TA
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TAT-TT TATTT TA
26183 CTGTTTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 24 0.73
6 9 0.27
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (5 bp):
TATTT
Found at i:27434 original size:22 final size:23
Alignment explanation
Indices: 27396--27439 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
27386 AAGAAAAGGA
27396 AAAGGAAAAGAAAATAACAAAAG
1 AAAGGAAAAGAAAATAACAAAAG
*
27419 AAAGTAAAA-AAAATAACAAAA
1 AAAGGAAAAGAAAATAACAAAA
27440 ACCAAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.77, C:0.05, G:0.11, T:0.07
Consensus pattern (23 bp):
AAAGGAAAAGAAAATAACAAAAG
Found at i:32517 original size:21 final size:21
Alignment explanation
Indices: 32491--32539 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
32481 TAGGTCCTTA
32491 TATTTTGTGTTTAT-TTTAATT
1 TATTTTGTG-TTATCTTTAATT
*
32512 TATTTTGTGTTATCTTTATTT
1 TATTTTGTGTTATCTTTAATT
32533 TACTTTT
1 TA-TTTT
32540 TTATTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.16, C:0.04, G:0.08, T:0.71
Consensus pattern (21 bp):
TATTTTGTGTTATCTTTAATT
Found at i:33421 original size:21 final size:21
Alignment explanation
Indices: 33397--33440 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33387 CCAGAGGAGG
* *
33397 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAACT
* *
33418 AGGAGCAGCTCGTGAAGAACT
1 AGGAGCAGCACGAGAAGAACT
33439 AG
1 AG
33441 CTCCCGGGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAACT
Found at i:37330 original size:39 final size:39
Alignment explanation
Indices: 37274--37429 Score: 131
Period size: 39 Copynumber: 4.0 Consensus size: 39
37264 ACTAACTACC
* * * *
37274 GCATGCTCCTCA-ACTTTGTGCTCAGGGTATGTCCTTACT
1 GCATGCTCCT-ATGCTTTGTGCTCAGGATAAGACCTTACT
*
37313 GCATGCTCCTATGCTTTGTACAT-AGGATAAGACCTTACT
1 GCATGCTCCTATGCTTTGTGC-TCAGGATAAGACCTTACT
* * *
37352 GCA-GACTCCTCTGCTTTGTGCACAAGATAAGACCTTACT
1 GCATG-CTCCTATGCTTTGTGCTCAGGATAAGACCTTACT
* * * * *
37391 GCAGGCTCCTCTGCTTTATGCACAAGG-TAAGCCCTTACT
1 GCATGCTCCTATGCTTTGTGCTC-AGGATAAGACCTTACT
37430 AGGTGTACAT
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
38 2 0.02
39 93 0.94
40 4 0.04
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (39 bp):
GCATGCTCCTATGCTTTGTGCTCAGGATAAGACCTTACT
Found at i:42439 original size:18 final size:18
Alignment explanation
Indices: 42416--42468 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
42406 TTCGACCATT
42416 GATCGTTGACCATTGACC
1 GATCGTTGACCATTGACC
42434 GATCGTTGACCATTGACC
1 GATCGTTGACCATTGACC
*
42452 GACCGTTGACCATTGAC
1 GATCGTTGACCATTGAC
42469 TTTGACCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (18 bp):
GATCGTTGACCATTGACC
Found at i:43066 original size:205 final size:205
Alignment explanation
Indices: 42714--43133 Score: 759
Period size: 205 Copynumber: 2.0 Consensus size: 205
42704 AGTTAGATTC
42714 GGTGTTTCCCGTCTGTCAGATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTCCGTA
1 GGTGTTTCCCGTCTGTCAGATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTCCGTA
42779 AATTATTTAAATAAAGGTTAATATTATTCATATTATGATTCCAATATAAATTTTCTGATTCATAG
66 AATTATTTAAATAAAGGTTAATATTATTCATATTATGATTCCAATATAAATTTTCTGATTCATAG
*
42844 GATCTAGCATTGCCGCTGATCGTGATCGACAAACTCAGTAGTAAGCTTTCGTATCAGACTACTTA
131 GATCTAGCATTGCCGCTGATCGTGATCGACAAACTCAGTAGTAAGCTTCCGTATCAGACTACTTA
42909 GATCGATATA
196 GATCGATATA
* *
42919 GGTGTTTCCGGTCTGTCAGATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTTCGTA
1 GGTGTTTCCCGTCTGTCAGATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTCCGTA
* * *
42984 AATTATTTAAATAAAGGTTAATATTATTCATATTATGATTCCAATATAGATTTTCTTATTCGTAG
66 AATTATTTAAATAAAGGTTAATATTATTCATATTATGATTCCAATATAAATTTTCTGATTCATAG
* *
43049 GATCTAGCATTGCCGCTGATCGTGATCGACAAACTCAGTAGTAGGCTTCCTTATCAGACTACTTA
131 GATCTAGCATTGCCGCTGATCGTGATCGACAAACTCAGTAGTAAGCTTCCGTATCAGACTACTTA
43114 GATCGATATA
196 GATCGATATA
43124 GGTGTCTTCC
1 GGTGT-TTCC
43134 TGTTAGTGTT
Statistics
Matches: 206, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
205 202 0.98
206 4 0.02
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (205 bp):
GGTGTTTCCCGTCTGTCAGATGTGCTCAATCCATATTTTACGAGAGATACCCATAGGTTTCCGTA
AATTATTTAAATAAAGGTTAATATTATTCATATTATGATTCCAATATAAATTTTCTGATTCATAG
GATCTAGCATTGCCGCTGATCGTGATCGACAAACTCAGTAGTAAGCTTCCGTATCAGACTACTTA
GATCGATATA
Found at i:43547 original size:39 final size:39
Alignment explanation
Indices: 43522--43645 Score: 160
Period size: 39 Copynumber: 3.2 Consensus size: 39
43512 CGGGGTATGT
* *
43522 CCTTACTGTAGGCTCCTCTGTTTTGTGCACAAGATAAGA
1 CCTTACTGCAGGCTCCTCTGCTTTGTGCACAAGATAAGA
* *
43561 CCTTACTGCAGGCTCCTCTGCTTTGTGCACATGATATGA
1 CCTTACTGCAGGCTCCTCTGCTTTGTGCACAAGATAAGA
* * * *
43600 CCTTA-TCGCAGGCTCCTATGCTTTGTGCACAGGGTAAGC
1 CCTTACT-GCAGGCTCCTCTGCTTTGTGCACAAGATAAGA
43639 CCTTACT
1 CCTTACT
43646 AGGTGTACAT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
38 1 0.01
39 72 0.97
40 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.32
Consensus pattern (39 bp):
CCTTACTGCAGGCTCCTCTGCTTTGTGCACAAGATAAGA
Found at i:43604 original size:78 final size:78
Alignment explanation
Indices: 43490--43645 Score: 179
Period size: 78 Copynumber: 2.0 Consensus size: 78
43480 AGTTCTAACC
* * * * * * * *
43490 GCAGGCTCTTCGGCTTTGTGCTCGGGGTATGTCCTTA-CTGTAGGCTCCTCTGTTTTGTGCACAA
1 GCAGGCTCCTCGGCTTTGTGCACAGGATATGACCTTATC-GCAGGCTCCTATGCTTTGTGCACAA
43554 GATAAGACCTTACT
65 GATAAGACCTTACT
* * *
43568 GCAGGCTCCTCTGCTTTGTGCACATGATATGACCTTATCGCAGGCTCCTATGCTTTGTGCACAGG
1 GCAGGCTCCTCGGCTTTGTGCACAGGATATGACCTTATCGCAGGCTCCTATGCTTTGTGCACAAG
* *
43633 GTAAGCCCTTACT
66 ATAAGACCTTACT
43646 AGGTGTACAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
78 63 0.98
79 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (78 bp):
GCAGGCTCCTCGGCTTTGTGCACAGGATATGACCTTATCGCAGGCTCCTATGCTTTGTGCACAAG
ATAAGACCTTACT
Found at i:48356 original size:43 final size:44
Alignment explanation
Indices: 48233--48360 Score: 134
Period size: 43 Copynumber: 2.9 Consensus size: 44
48223 ACGATCTACC
* * * *
48233 TCCTTCTATGATAGAATCAAATAAAATAAGATTATGTTGATTCAAA
1 TCCTTCTATGA-AGAATCAAACAAAATAA-CTAATGTTGATCCAAA
* * * * *
48279 TACTTCTGTGAAGAATCAAGCAGAATGAC-AATGTTGATCCAAA
1 TCCTTCTATGAAGAATCAAACAAAATAACTAATGTTGATCCAAA
*
48322 TCCTTCTATGAAGAATCAAACAAAAT-ACTGATGTTGATC
1 TCCTTCTATGAAGAATCAAACAAAATAACTAATGTTGATC
48361 TGCCTCTTTC
Statistics
Matches: 67, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
42 2 0.03
43 43 0.64
45 13 0.19
46 9 0.13
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (44 bp):
TCCTTCTATGAAGAATCAAACAAAATAACTAATGTTGATCCAAA
Found at i:49654 original size:5 final size:5
Alignment explanation
Indices: 49641--49728 Score: 81
Period size: 5 Copynumber: 16.8 Consensus size: 5
49631 TATTTTCCTT
*
49641 TTTTC -TTTC TTTTC TTTTTC TTTTCC TTTTAT TTTTC TTTTC TTTTCC
1 TTTTC TTTTC TTTTC -TTTTC TTTT-C TTTT-C TTTTC TTTTC TTTT-C
* *
49689 TTTTC TTTT- TATCTC CTTTC TTTTC TTCTTC TTTTC TTTT
1 TTTTC TTTTC T-TTTC TTTTC TTTTC TT-TTC TTTTC TTTT
49729 TTCCTTTTCT
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
4 5 0.07
5 40 0.58
6 24 0.35
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTC
Found at i:49659 original size:16 final size:16
Alignment explanation
Indices: 49633--49731 Score: 69
Period size: 17 Copynumber: 5.8 Consensus size: 16
49623 CCCTTTTTTA
49633 TTTTCCTTTTTTCTTTC
1 TTTT-CTTTTTTCTTTC
49650 TTTTC-TTTTTCTTTTCC
1 TTTTCTTTTTTC-TTT-C
*
49667 TTTT-ATTTTTCTTTTC
1 TTTTCTTTTTTC-TTTC
*
49683 TTTTCCTTTTCTTTTTATC
1 TTTT-CTTTT-TTCTT-TC
49702 TCCTTTCTTTTCTTC-TTC
1 T--TTTCTTTT-TTCTTTC
49720 TTTTCTTTTTTC
1 TTTTCTTTTTTC
49732 CTTTTCTTCT
Statistics
Matches: 70, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
15 9 0.13
16 17 0.24
17 19 0.27
18 8 0.11
19 6 0.09
20 8 0.11
21 3 0.04
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTTTCTTTC
Found at i:49666 original size:28 final size:29
Alignment explanation
Indices: 49627--49729 Score: 129
Period size: 28 Copynumber: 3.6 Consensus size: 29
49617 TTTAACCCCT
*
49627 TTTTTATTTTCCTTTT-TTCTTTCTTTTC
1 TTTTTCTTTTCCTTTTATTCTTTCTTTTC
49655 TTTTTCTTTTCCTTTTATT-TTTCTTTTC
1 TTTTTCTTTTCCTTTTATTCTTTCTTTTC
* *
49683 TTTTCCTTTTCTTTTTATCTCCTTTCTTTTC
1 TTTTTCTTTTCCTTTTAT-T-CTTTCTTTTC
* *
49714 TTCTTCTTTTCTTTTT
1 TTTTTCTTTTCCTTTT
49730 TCCTTTTCTT
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
28 40 0.61
29 3 0.05
31 23 0.35
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTTCTTTTCCTTTTATTCTTTCTTTTC
Found at i:49691 original size:11 final size:11
Alignment explanation
Indices: 49646--49739 Score: 79
Period size: 11 Copynumber: 8.5 Consensus size: 11
49636 TCCTTTTTTC
*
49646 TTTCTTTTCTT
1 TTTCTTTTCCT
49657 TTTCTTTTCCT
1 TTTCTTTTCCT
* *
49668 TTTATTTTTCT
1 TTTCTTTTCCT
49679 TTTCTTTTCCT
1 TTTCTTTTCCT
49690 TTTCTTTT--T
1 TTTCTTTTCCT
* *
49699 ATCTCCTTT-CT
1 -TTTCTTTTCCT
49710 TTTCTTCTT-CT
1 TTTCTT-TTCCT
49721 TTTCTTTTTTCCT
1 TTTC--TTTTCCT
49734 TTTCTT
1 TTTCTT
49740 CTTCAAGTAT
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
9 1 0.01
10 10 0.15
11 47 0.69
12 2 0.03
13 8 0.12
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTCTTTTCCT
Found at i:49742 original size:16 final size:16
Alignment explanation
Indices: 49628--49739 Score: 92
Period size: 16 Copynumber: 7.1 Consensus size: 16
49618 TTAACCCCTT
* *
49628 TTTTATTTTCCTTTTT
1 TTTTCTTTTCCTTTTC
*
49644 TCTTTCTTTTCTTTTTC
1 T-TTTCTTTTCCTTTTC
**
49661 TTTTCCTTTTATTTTTC
1 TTTT-CTTTTCCTTTTC
49678 TTTTCTTTTCCTTTTC
1 TTTTCTTTTCCTTTTC
*
49694 TTTT-TATCTCC-TTTC
1 TTTTCT-TTTCCTTTTC
49709 TTTTCTTCTT-CTTTTC
1 TTTTCTT-TTCCTTTTC
49725 --TT-TTTTCCTTTTC
1 TTTTCTTTTCCTTTTC
49738 TT
1 TT
49740 CTTCAAGTAT
Statistics
Matches: 79, Mismatches: 8, Indels: 19
0.75 0.08 0.18
Matches are distributed among these distances:
12 2 0.03
13 8 0.10
14 2 0.03
15 11 0.14
16 28 0.35
17 28 0.35
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCTTTTCCTTTTC
Found at i:61335 original size:69 final size:69
Alignment explanation
Indices: 61224--61357 Score: 243
Period size: 69 Copynumber: 1.9 Consensus size: 69
61214 ATCTTGGGCA
*
61224 GGTTTATGTAAAAGCTTCTTACTTCGATACAATCCACCCAATATGAATACAC-AGCTACATAATG
1 GGTTTATATAAAAGCTTCTTACTTCGATACAATCCACCCAATATGAATACACGA-CTACATAATG
61288 ATGCG
65 ATGCG
61293 GGTTTATATAAAAGCTTCTTACTTCGATACAATCCACCCAATATGAATACACGACTACATAATGA
1 GGTTTATATAAAAGCTTCTTACTTCGATACAATCCACCCAATATGAATACACGACTACATAATGA
61358 CATTGCAATT
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
69 62 0.98
70 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.29
Consensus pattern (69 bp):
GGTTTATATAAAAGCTTCTTACTTCGATACAATCCACCCAATATGAATACACGACTACATAATGA
TGCG
Found at i:66589 original size:24 final size:24
Alignment explanation
Indices: 66544--66593 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
66534 TGGGGGTTGG
66544 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
66568 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
66592 TT
1 TT
66594 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Done.