Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002791.1 Hibiscus syriacus cultivar Beakdansim tig00005751_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: 109280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1984 original size:22 final size:23
Alignment explanation
Indices: 1944--2005 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
1934 TAAAATATTT
*
1944 AAAATATATTTATTAATATTTCTA
1 AAAATATA-ATATTAATATTTCTA
*
1968 AAAATATAATATT-ATATTTTTA
1 AAAATATAATATTAATATTTCTA
* * *
1990 ATATTATAATAATAAT
1 AAAATATAATATTAAT
2006 CAATTATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 18 0.56
23 6 0.19
24 8 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATATTAATATTTCTA
Found at i:2304 original size:20 final size:20
Alignment explanation
Indices: 2277--2320 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2267 ATTTTATTAA
2277 TAAT-ATAAAAAAAATATTT
1 TAATAATAAAAAAAATATTT
** *
2296 TAATAATAAGTAAATTATTT
1 TAATAATAAAAAAAATATTT
2316 TAATA
1 TAATA
2321 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TAATAATAAAAAAAATATTT
Found at i:3961 original size:16 final size:15
Alignment explanation
Indices: 3935--3966 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3925 GCAATAAAAA
3935 TAATATCAATCAAAT
1 TAATATCAATCAAAT
3950 TAATATTCAATCAAAT
1 TAATA-TCAATCAAAT
3966 T
1 T
3967 GTTGTACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATATCAATCAAAT
Found at i:6933 original size:15 final size:15
Alignment explanation
Indices: 6913--6944 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6903 ACATTATTAT
*
6913 TAAACTAAGTTACAC
1 TAAACTAAGTTAAAC
6928 TAAACTAAGTTAAAC
1 TAAACTAAGTTAAAC
6943 TA
1 TA
6945 CGAGCGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (15 bp):
TAAACTAAGTTAAAC
Found at i:13361 original size:25 final size:26
Alignment explanation
Indices: 13327--13400 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 26
13317 CGTATAATTA
* *
13327 CACCGTAGTGCCACGTAGAATTTTG-
1 CACCGAAGTGCCGCGTAGAATTTTGT
*
13352 CACCGAAGTGCCGCGTAGAAATTTGT
1 CACCGAAGTGCCGCGTAGAATTTTGT
*
13378 CCCCGAAG-GACCGCGTAGAATTT
1 CACCGAAGTG-CCGCGTAGAATTT
13401 ATCCCGAAGG
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
25 23 0.55
26 19 0.45
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (26 bp):
CACCGAAGTGCCGCGTAGAATTTTGT
Found at i:13383 original size:26 final size:26
Alignment explanation
Indices: 13333--13409 Score: 81
Period size: 25 Copynumber: 3.1 Consensus size: 26
13323 ATTACACCGT
* * *
13333 AGTGCCACGTAGAATTTTG-CACCGA
1 AGTGCCGCGTAGAAATTTGTCCCCGA
13358 AGTGCCGCGTAGAAATTTGTCCCCGA
1 AGTGCCGCGTAGAAATTTGTCCCCGA
*
13384 AG-GACCGCGTAG-AATTTAT-CCCGA
1 AGTG-CCGCGTAGAAATTTGTCCCCGA
13408 AG
1 AG
13410 GACCACATAG
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
24 7 0.15
25 24 0.52
26 15 0.33
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (26 bp):
AGTGCCGCGTAGAAATTTGTCCCCGA
Found at i:13411 original size:24 final size:24
Alignment explanation
Indices: 13340--13413 Score: 80
Period size: 26 Copynumber: 3.0 Consensus size: 24
13330 CGTAGTGCCA
*
13340 CGTAGAATTTTGCACCGAAGTG-CCG
1 CGTAGAATTTT-CCCCGAAG-GACCG
13365 CGTAGAAATTTGTCCCCGAAGGACCG
1 CGTAG-AATTT-TCCCCGAAGGACCG
13391 CGTAGAATTTAT-CCCGAAGGACC
1 CGTAGAATTT-TCCCCGAAGGACC
13414 ACATAGAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 11 0.25
25 12 0.27
26 20 0.45
27 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.22
Consensus pattern (24 bp):
CGTAGAATTTTCCCCGAAGGACCG
Found at i:13424 original size:25 final size:26
Alignment explanation
Indices: 13367--13424 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
13357 AAGTGCCGCG
* * *
13367 TAGAAATTTGTCCCCGAAGGACCGCG
1 TAGAAATTTATCCCCGAAGGACCACA
13393 TAG-AATTTAT-CCCGAAGGACCACA
1 TAGAAATTTATCCCCGAAGGACCACA
13417 TAGAAATT
1 TAGAAATT
13425 CCTTAAGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.54
25 10 0.36
26 3 0.11
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (26 bp):
TAGAAATTTATCCCCGAAGGACCACA
Found at i:13624 original size:15 final size:17
Alignment explanation
Indices: 13590--13627 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
13580 ATTGTCATTT
13590 CACATA-TTCATATATA
1 CACATAGTTCATATATA
13606 CACATAGTTCA-AT-TA
1 CACATAGTTCATATATA
13621 CACATAG
1 CACATAG
13628 AACATTTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 8 0.38
17 4 0.19
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (17 bp):
CACATAGTTCATATATA
Found at i:17719 original size:264 final size:257
Alignment explanation
Indices: 17269--17770 Score: 728
Period size: 264 Copynumber: 1.9 Consensus size: 257
17259 CTCCAACCGA
17269 GACCCGACCCGACCAAAATAAAGTTTCATCCGACCAACCCGAATATATGAATAAGAAACCCGACC
1 GACCCGACCCGACCAAAATAAAGTTTCA-CC-ACCAACCCGAATATATGAATAAGAAACCCGACC
**
17334 CGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGGGAAAAATAT
64 CGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAAAATAT
* *
17399 ATATAGAGAGGGATATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATTTTTTTGG
129 ATATAGAGAGAGATATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATA----TAT-G
*
17464 TCGGATCGGGTTGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAA
189 T----TCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAA
17529 AAAAAACC
250 AAAAAACC
* * *
17537 GACCCGACCCGACCAAAATAAAGTTTCA-C-CCAACCCGAATATATGAATTAGAAATCCGACCTG
1 GACCCGACCCGACCAAAATAAAGTTTCACCACCAACCCGAATATATGAATAAGAAACCCGACCCG
17600 ACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAACA-A-TGACTTAATTGAAAAAAACTAT
66 ACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAA-ATAGTGACTTAATTGAAAAAAA-TAT
*
17663 ATATAGAG-GAG-TATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATATGTTC
129 ATATAGAGAGAGATATTATTATAATTATTCCTAAATATATAAGGTAAAA-T-TATATATATGTTC
* *
17726 GGGTCGGGTATTTTTCACCCTAAACCTGAACTCGACCCGACCCGA
192 GGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGA
17771 CCAAAATAAA
Statistics
Matches: 219, Mismatches: 11, Indels: 21
0.87 0.04 0.08
Matches are distributed among these distances:
255 44 0.20
259 2 0.01
260 2 0.01
262 35 0.16
263 19 0.09
264 87 0.40
265 1 0.00
266 1 0.00
268 28 0.13
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.27
Consensus pattern (257 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCACCAACCCGAATATATGAATAAGAAACCCGACCCG
ACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAATAGTGACTTAATTGAAAAAAATATAT
ATAGAGAGAGATATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATATGTTCGGGT
CGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATATCACACTTAAAAAAAACC
Found at i:26505 original size:19 final size:18
Alignment explanation
Indices: 26477--26512 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
26467 TAATTTGAAT
26477 ATTAACTATATATATTATC
1 ATTAACTATA-ATATTATC
*
26496 ATTAATTATAATATTAT
1 ATTAACTATAATATTAT
26513 ATATATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAACTATAATATTATC
Found at i:26513 original size:23 final size:22
Alignment explanation
Indices: 26487--26540 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
26477 ATTAACTATA
26487 TATATTATCATTAATTAT-AATAT
1 TATATTATCA-TAATT-TGAATAT
*
26510 TATATATATTATAATTTGAATAT
1 TATAT-TATCATAATTTGAATAT
*
26533 TAAATTAT
1 TATATTAT
26541 TTTTAATGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.15
23 19 0.70
24 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TATATTATCATAATTTGAATAT
Found at i:27727 original size:20 final size:20
Alignment explanation
Indices: 27704--27809 Score: 117
Period size: 20 Copynumber: 5.2 Consensus size: 20
27694 GAATATGTAA
*
27704 ATCGCAACGCGATTTTGACT
1 ATCGCAACGCGATTATGACT
*
27724 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTATGAC-T
*
27744 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTATGACT
*
27765 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTATGAC-T
*
27785 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTATGACT
27806 ATCG
1 ATCG
27810 TGTTGCGATA
Statistics
Matches: 72, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
19 4 0.06
20 34 0.47
21 30 0.42
22 4 0.06
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:27822 original size:41 final size:41
Alignment explanation
Indices: 27703--27809 Score: 205
Period size: 41 Copynumber: 2.6 Consensus size: 41
27693 TGAATATGTA
*
27703 AATCGCAACGCGATTTTGACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
27744 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
1 AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
27785 AATCGCAACGCGATTCTGACTATCG
1 AATCGCAACGCGATTCTGACTATCG
27810 TGTTGCGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (41 bp):
AATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAT
Found at i:27830 original size:41 final size:41
Alignment explanation
Indices: 27702--27840 Score: 197
Period size: 41 Copynumber: 3.4 Consensus size: 41
27692 GTGAATATGT
*
27702 AAATCGCAACGCGATTTTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
*
27743 TAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
* **** *
27784 TAATCGCAACGCGATTCTGACTATCGTGTTGCGATAATAGA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
*
27825 AAATCGCAATGCGATT
1 AAATCGCAACGCGATT
27841 TTCAAAGCGC
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
Found at i:28314 original size:39 final size:39
Alignment explanation
Indices: 28225--28327 Score: 107
Period size: 39 Copynumber: 2.6 Consensus size: 39
28215 AAAATCGCAA
* ** *
28225 CGATAGTCAAATTCGAGTTGCGATAGTCATTTTCGTGTTG
1 CGATAGTC-ATTTCGAGTTGCGATAGTCAAATTCGCGTTG
* ** *
28265 CGCTTTTCATTTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTCGAGTTGCGATAGTCAAATTCGCGTTG
*
28304 CGATAGTCATTTTCGTGTTGCGAT
1 CGATAGTCA-TTTCGAGTTGCGAT
28328 TTTCATTTTC
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
39 32 0.64
40 18 0.36
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (39 bp):
CGATAGTCATTTCGAGTTGCGATAGTCAAATTCGCGTTG
Found at i:28317 original size:59 final size:60
Alignment explanation
Indices: 28225--28347 Score: 212
Period size: 59 Copynumber: 2.1 Consensus size: 60
28215 AAAATCGCAA
*
28225 CGATAGTCAAATTCGAGTTGCGATAGTCATTTTCGTGTTGCGCTTTTCA-TTTCGCGTTG
1 CGATAGTCAAATTCGAGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTG
* *
28284 CGATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGTGTTG
1 CGATAGTCAAATTCGAGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTG
28344 CGAT
1 CGAT
28348 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
59 47 0.78
60 13 0.22
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41
Consensus pattern (60 bp):
CGATAGTCAAATTCGAGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTTTCGCGTTG
Found at i:28350 original size:20 final size:20
Alignment explanation
Indices: 28225--28347 Score: 131
Period size: 20 Copynumber: 6.2 Consensus size: 20
28215 AAAATCGCAA
** *
28225 CGATAGTCAAATTCGAGTTG
1 CGATAGTCATTTTCGTGTTG
28245 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGTGTTG
* ** *
28265 CGCTTTTCA-TTTCGCGTTG
1 CGATAGTCATTTTCGTGTTG
** *
28284 CGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGTGTTG
28304 CGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGTGTTG
**
28324 CGATTTTCATTTTCGTGTTG
1 CGATAGTCATTTTCGTGTTG
28344 CGAT
1 CGAT
28348 TTTAAGTTTC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
19 15 0.17
20 71 0.83
ACGTcount: A:0.17, C:0.18, G:0.24, T:0.41
Consensus pattern (20 bp):
CGATAGTCATTTTCGTGTTG
Found at i:28357 original size:20 final size:20
Alignment explanation
Indices: 28314--28357 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
28304 CGATAGTCAT
* *
28314 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
28334 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
28354 TTTC
1 TTTC
28358 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:30093 original size:11 final size:11
Alignment explanation
Indices: 30058--30105 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
30048 TTTCATATAT
*
30058 ATTTAACTT-G
1 ATTTCACTTAG
*
30068 ATTTACACGTA-
1 ATTT-CACTTAG
30079 ATTTCACTTAG
1 ATTTCACTTAG
30090 ATTTCACTTAG
1 ATTTCACTTAG
30101 ATTTC
1 ATTTC
30106 TTAGTAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (11 bp):
ATTTCACTTAG
Found at i:30293 original size:20 final size:20
Alignment explanation
Indices: 30264--30332 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
30254 AAACTTAAAA
30264 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * *
30284 ATCACAACGCGGAAATGATT
1 ATCGCAACGCGAAAATGACT
* **
30304 ATTGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
30324 ATCGCAACG
1 ATCGCAACG
30333 GGATAATCGT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:30374 original size:33 final size:34
Alignment explanation
Indices: 30324--30399 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 34
30314 GAATTTGACT
* *
30324 ATCGCAACGGGATAATCGTAATGC-AAAATAAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
* *
30357 ATCGCAACGTGAAAATCGCAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
30391 ATCGCAACG
1 ATCGCAACG
30400 CGAATTTAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
33 21 0.55
34 17 0.45
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGCAATGCGAAAATAAAA
Found at i:30389 original size:20 final size:20
Alignment explanation
Indices: 30366--30403 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
30356 AATCGCAACG
*
30366 TGAAAATCGCAATGCGAAAA
1 TGAAAATCGCAACGCGAAAA
30386 TGAAAATCGCAACGCGAA
1 TGAAAATCGCAACGCGAA
30404 TTTAGTTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (20 bp):
TGAAAATCGCAACGCGAAAA
Found at i:30421 original size:19 final size:19
Alignment explanation
Indices: 30399--30443 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
30389 AAATCGCAAC
30399 GCGAATTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
30418 GCGATTTTGGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
30437 GC-AATTT
1 GCGAATTT
30444 TTATTTCGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.13, C:0.16, G:0.27, T:0.44
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:30450 original size:19 final size:19
Alignment explanation
Indices: 30404--30457 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
30394 GCAACGCGAA
*
30404 TTTAGTTTCGCGTTGCGATT
1 TTTA-TTTCGCGTTGCAATT
**
30424 TTGGTTTCGCGTTGCAATT
1 TTTATTTCGCGTTGCAATT
*
30443 TTTATTTCGCATTGC
1 TTTATTTCGCGTTGC
30458 GATTATCCCG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 26 0.93
20 2 0.07
ACGTcount: A:0.11, C:0.17, G:0.22, T:0.50
Consensus pattern (19 bp):
TTTATTTCGCGTTGCAATT
Found at i:30491 original size:20 final size:20
Alignment explanation
Indices: 30466--30514 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
30456 GCGATTATCC
30466 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
30486 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
30506 CGTTGCGAT
1 CGTTGCGAT
30515 TTTAAGTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:30524 original size:20 final size:20
Alignment explanation
Indices: 30501--30544 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
30491 CGATAGTCAT
30501 TTTCGCGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
30521 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
30541 TTTC
1 TTTC
30545 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:31101 original size:42 final size:42
Alignment explanation
Indices: 31037--31148 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 42
31027 CTGTTATCAT
* *
31037 TCAAGAGG-CCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGTCC-CTCCCACCGTTCAAGAGGCCCCTATCATCCC
**
31079 TCAAGA-GTCCCTTCCCACCGTTCAAGAGGCCCCTATCATCGT
1 TCAAGAGGTCCC-TCCCACCGTTCAAGAGGCCCCTATCATCCC
* *
31121 TGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCAAGAGGTCCCTCCCACCGTTCAAGAG
31149 CCCGATTCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
41 2 0.03
42 54 0.89
43 5 0.08
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (42 bp):
TCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:31121 original size:21 final size:21
Alignment explanation
Indices: 31036--31148 Score: 84
Period size: 21 Copynumber: 5.4 Consensus size: 21
31026 CCTGTTATCA
*
31036 TTCAAGAGGCCTCT-CCTATCG
1 TTCAAGAGGCCCCTACC-ATCG
* *
31057 TTCAAGAGGCCCCTATCATCC
1 TTCAAGAGGCCCCTACCATCG
* * * * *
31078 CTCAAGAGTCCCTTCCCACCG
1 TTCAAGAGGCCCCTACCATCG
*
31099 TTCAAGAGGCCCCTATCATCG
1 TTCAAGAGGCCCCTACCATCG
* * * * *
31120 TTGAAGAGGTCCCTCCCACCA
1 TTCAAGAGGCCCCTACCATCG
31141 TTCAAGAG
1 TTCAAGAG
31149 CCCGATTCAT
Statistics
Matches: 68, Mismatches: 23, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
21 67 0.99
22 1 0.01
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTACCATCG
Found at i:33352 original size:14 final size:14
Alignment explanation
Indices: 33333--33359 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
33323 TCCTGTGGCA
33333 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
33347 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
33360 TTTCATCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:33583 original size:24 final size:24
Alignment explanation
Indices: 33556--33609 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
33546 TTGAAACATC
*
33556 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
33580 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
33604 ATCAAA
1 ATCAAA
33610 TTTTGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:34476 original size:20 final size:20
Alignment explanation
Indices: 34429--34517 Score: 99
Period size: 20 Copynumber: 4.4 Consensus size: 20
34419 GAAATTCAGT
* *
34429 GTTGCGACAGTCAGAATCGT
1 GTTGCGATAGTCAGAATCGC
34449 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
**
34469 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
* *
34490 ATTGCGATAGTCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
34510 GTTGCGAT
1 GTTGCGAT
34518 TTACATATTC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 39 0.68
21 14 0.25
22 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:34606 original size:41 final size:41
Alignment explanation
Indices: 34450--34658 Score: 124
Period size: 41 Copynumber: 5.2 Consensus size: 41
34440 CAGAATCGTG
* * **
34450 TTGCGATAGTCAGAATCGCGTTGCG-ATTATGTATTATCGCA
1 TTGCGATAGTCAAAATCGCGTTGCGAATT-TGGAAAATCGCA
* * ** * *
34491 TTGCGATAGTCAGAATCACGTTGCG-ATTTACATATTCGCA
1 TTGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCA
** *** *
34531 TTGCGATTTTCTAAAATCGCAACGCAAATTTGGAAAATCGCA
1 TTGCGATAGTC-AAAATCGCGTTGCGAATTTGGAAAATCGCA
* * *
34573 ATGCGATAGTCAAAATCGCGTTGCGAATCTGGAAACT-G-A
1 TTGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCA
* ** * * *
34612 TTTGCGATACTGGAGATCGCGTTGCG-ATTTAG-AGATCGCA
1 -TTGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCA
34652 TTGCGAT
1 TTGCGAT
34659 TTTGTTGGTC
Statistics
Matches: 128, Mismatches: 35, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
38 2 0.02
39 13 0.10
40 39 0.30
41 55 0.43
42 19 0.15
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (41 bp):
TTGCGATAGTCAAAATCGCGTTGCGAATTTGGAAAATCGCA
Found at i:34636 original size:20 final size:19
Alignment explanation
Indices: 34613--34658 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
34603 GGAAACTGAT
* *
34613 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
34633 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
34652 TTGCGAT
1 TTGCGAT
34659 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:34648 original size:19 final size:19
Alignment explanation
Indices: 34624--34660 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
34614 TGCGATACTG
*
34624 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
34643 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
34661 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:34797 original size:2 final size:2
Alignment explanation
Indices: 34786--34839 Score: 50
Period size: 2 Copynumber: 30.0 Consensus size: 2
34776 ATATTCAAAT
34786 TA TA -A TA TA TA TA TA TA TA T- TA TA -A T- TA -A TGA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
34823 TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA
34840 GTTATTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
1 7 0.16
2 35 0.80
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:36813 original size:32 final size:32
Alignment explanation
Indices: 36772--36884 Score: 138
Period size: 32 Copynumber: 3.5 Consensus size: 32
36762 ACTGACGCTC
* *
36772 TTGTGCATTATATGAATGTAATAACGACTATG
1 TTGTGCATTATCTGAATGTAATAACGACTTTG
* * *
36804 TTGTGCATTATCTGAATATAAT-ACTAGCTTTA
1 TTGTGCATTATCTGAATGTAATAACGA-CTTTG
* * *
36836 CTGTGCATTATCTGAATGCAATAATGACTTTG
1 TTGTGCATTATCTGAATGTAATAACGACTTTG
36868 TTGTGCATTATCTGAAT
1 TTGTGCATTATCTGAAT
36885 ACAACACTGA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 3 0.04
32 62 0.93
33 2 0.03
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (32 bp):
TTGTGCATTATCTGAATGTAATAACGACTTTG
Found at i:38814 original size:21 final size:22
Alignment explanation
Indices: 38771--38815 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
38761 CTCAAAGTGA
**
38771 TTAGAAACATATTTCTAAACAC
1 TTAGAAACATATTTAGAAACAC
*
38793 TTAGAAACA-ATTTAGAACCAC
1 TTAGAAACATATTTAGAAACAC
38814 TT
1 TT
38816 TTAAGCCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (22 bp):
TTAGAAACATATTTAGAAACAC
Found at i:51192 original size:21 final size:24
Alignment explanation
Indices: 51143--51196 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
51133 ATTTAACAAA
*
51143 AAGGGGGAGAAGTGTTAAGGTGTT
1 AAGGGGGAGAAGTGTTAAGGAGTT
51167 AAGGGGGAGAAGTGTT-A-GAG-T
1 AAGGGGGAGAAGTGTTAAGGAGTT
51188 AAGGGGGAG
1 AAGGGGGAG
51197 TAATTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 10 0.34
22 2 0.07
23 1 0.03
24 16 0.55
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (24 bp):
AAGGGGGAGAAGTGTTAAGGAGTT
Found at i:51995 original size:34 final size:32
Alignment explanation
Indices: 51956--52025 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
51946 TTTTGTAAAG
* * *
51956 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
51990 GGGAAAGGTTATAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
52022 GGGA
1 GGGA
52026 GTTTGTAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:54850 original size:11 final size:11
Alignment explanation
Indices: 54834--54859 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54824 CAAATATTTC
54834 GACCGTTAGTT
1 GACCGTTAGTT
54845 GACCGTTAGTT
1 GACCGTTAGTT
54856 GACC
1 GACC
54860 TAGTGTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (11 bp):
GACCGTTAGTT
Found at i:57757 original size:100 final size:104
Alignment explanation
Indices: 57622--58039 Score: 288
Period size: 100 Copynumber: 4.0 Consensus size: 104
57612 ATATAAAAAT
* * * *
57622 ACTATTTATTTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTT-AGTAAGTTTAGTTTAAAT
1 ACTATTTATTTTTGATTTTACAGATTAAATAGTATTTAAGTAGTTTGA-TAAGTTTAGTTTAAAT
57686 TATA-T-TTTTA-TTTTTATTAAGT-AATATAAA-ATATTAG
65 TATATTGTTTTATTTTTTATT--GTAAATATAAATATATTAG
* *
57723 ACTAATTATTTTT-ATTTTACAGATTAAATAGTATTTAAGTGGTTTGATAAGTTTAGTTTAAATT
1 ACTATTTATTTTTGATTTTACAGATTAAATAGTATTTAAGTAGTTTGATAAGTTTAGTTTAAATT
* *
57787 TTATTGTTTTATTTTTTATTGTAAATATAAATTTATTAG
66 ATATTGTTTTATTTTTTATTGTAAATATAAATATATTAG
* *
57826 ACTATTTA-TTTTGATTGTTA-AG--T---T-GTATTTGAA-TGGTTTTG-TAAGTTTAATTTAA
1 ACTATTTATTTTTGATT-TTACAGATTAAATAGTATTT-AAGTAG-TTTGATAAGTTTAGTTTAA
* * *
57881 TTTTTCGTGTAATT-TTTAGTATAATTTTTATTTTTAAATATAAATTATAATTATTAG
63 ---AT--TAT-ATTGTTT--TAT--TTTTTA-TTGTAAATAT-AA--AT-A-TATTAG
* * * * *
57938 ACTATTTA-TTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTTGGTAAGTTTAGTTTAAATT
1 ACTATTTATTTTTGATTTTACAGATTAAATAGTATTTAAGTAGTTTGATAAGTTTAGTTTAAATT
*
58002 TTA-T-TTTTATTTTTTATTG-AGTAATATAAAT-TATTAG
66 ATATTGTTTTATTTTTTATTGTA--AATATAAATATATTAG
58039 A
1 A
58040 ATAAATGTGC
Statistics
Matches: 259, Mismatches: 21, Indels: 74
0.73 0.06 0.21
Matches are distributed among these distances:
97 22 0.08
98 7 0.03
100 47 0.18
101 24 0.09
102 22 0.08
103 29 0.11
104 8 0.03
105 1 0.00
106 10 0.04
107 20 0.08
108 2 0.01
109 3 0.01
110 2 0.01
111 7 0.03
112 24 0.09
113 2 0.01
114 1 0.00
115 1 0.00
117 6 0.02
118 21 0.08
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (104 bp):
ACTATTTATTTTTGATTTTACAGATTAAATAGTATTTAAGTAGTTTGATAAGTTTAGTTTAAATT
ATATTGTTTTATTTTTTATTGTAAATATAAATATATTAG
Found at i:59972 original size:71 final size:71
Alignment explanation
Indices: 59821--59980 Score: 182
Period size: 71 Copynumber: 2.3 Consensus size: 71
59811 GTTGTTCTTG
* * * ** **
59821 AAAATTTAAAAATTATTATATATTTTAATTTTTTTATATATTTTTTATTGAAAATTTGTTTATCG
1 AAAATTTTAAAATTATCATATATTTAAATTTTTTTATATATTTCCTATTGAAAATTAATTTATCG
59886 CCCTCT
66 CCCTCT
* *
59892 AAAAATTTAAAATTATCATATATTGTAAATTTTTTCTATATATTTCCTATTGAAAATTAATTTTT
1 AAAATTTTAAAATTATCATATATT-TAAATTTTTT-TATATATTTCCTATTGAAAATTAATTTAT
59957 C-CCC-CT
64 CGCCCTCT
* *
59963 AGAATTTT-AATTTATCAT
1 AAAATTTTAAAATTATCAT
59981 CCTTAAGTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
70 9 0.12
71 29 0.39
72 12 0.16
73 25 0.33
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (71 bp):
AAAATTTTAAAATTATCATATATTTAAATTTTTTTATATATTTCCTATTGAAAATTAATTTATCG
CCCTCT
Found at i:60040 original size:25 final size:25
Alignment explanation
Indices: 60006--60054 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
59996 CATCTCTCCT
60006 AATATAAAATCATGCGTCCGTCCCA
1 AATATAAAATCATGCGTCCGTCCCA
*
60031 AATATAAAATCATGCGTCTGTCCC
1 AATATAAAATCATGCGTCCGTCCC
60055 TATTTACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.27
Consensus pattern (25 bp):
AATATAAAATCATGCGTCCGTCCCA
Found at i:60402 original size:2 final size:2
Alignment explanation
Indices: 60395--60465 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
60385 GGCGTGAAAT
60395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
60437 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60466 GAGTTTCCAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61468 original size:29 final size:29
Alignment explanation
Indices: 61433--61514 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
61423 AAACTAAATT
*
61433 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
61462 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
61491 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
61515 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:66232 original size:29 final size:29
Alignment explanation
Indices: 66197--66278 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
66187 AAACTAAATT
*
66197 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
66226 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
66255 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
66279 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:67026 original size:2 final size:2
Alignment explanation
Indices: 67021--67059 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
67011 ACACACACAC
67021 AT AT 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 AT AT A
67060 AAGAAAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70118 original size:39 final size:38
Alignment explanation
Indices: 70013--70118 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 38
70003 TTTAAAAAAT
* * * * *
70013 AATTTAAAATTTTAAAGTGAAATAATTTGATAAATTAA
1 AATTTAGAATATTAGAGTGAAATAATTTAAGAAATTAA
*
70051 AATTTTAGAATGTTATG-GTGATAA-AATTTAAGAAATTAA
1 AA-TTTAGAATATTA-GAGTGA-AATAATTTAAGAAATTAA
70090 GAATTTAGAATATTAGAGTGAAATAATTT
1 -AATTTAGAATATTAGAGTGAAATAATTT
70119 GATTATTATA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
38 5 0.09
39 47 0.84
40 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (38 bp):
AATTTAGAATATTAGAGTGAAATAATTTAAGAAATTAA
Found at i:71901 original size:2 final size:2
Alignment explanation
Indices: 71894--71919 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
71884 GCTTTATGAA
71894 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
71920 GAGATAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72739 original size:22 final size:22
Alignment explanation
Indices: 72696--72739 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
72686 CAAATATAGG
* *
72696 AAAATATGTTATAAATACAAAA
1 AAAATATGTCATAAAGACAAAA
* *
72718 AAAATGTGTCATAAAGATAAAA
1 AAAATATGTCATAAAGACAAAA
72740 TTATTAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.61, C:0.05, G:0.09, T:0.25
Consensus pattern (22 bp):
AAAATATGTCATAAAGACAAAA
Found at i:75757 original size:101 final size:107
Alignment explanation
Indices: 75196--75880 Score: 479
Period size: 101 Copynumber: 6.4 Consensus size: 107
75186 TTTTTTTTTG
* * * * * **
75196 AAATATAAATTAATTATATTATTTATTTTGATTTTACATATTAAATTGTATTGGAGTTGTTTGGT
1 AAATATAAATT-ATTAGACTATTTATTTTGATTTTACAGATTAAATCGTATTTGAGTAATTTGGT
* * * * * * *
75261 AAGTTTAATTTAAATTTTCGTGTAATTTTTAGAATACTTTTATTTTTAATTT
65 AAGTTTAGTTTAAATTTT-AT-T--GTTTT-G-AT--TTTT-GTATTGATGT
* * * * * *
75313 AAAT-TATAATTATTATACTATTTATTTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTTAG
1 AAATATA-AATTATTAGACTATTTA-TTTTGATTTTACAGATTAAATCGTATTTGAGTAATTTGG
*
75377 TAAGTTTAGTTTAAATTATA-T-TTTT-A-TTTT-TATTGA-GT
64 TAAGTTTAGTTTAAATTTTATTGTTTTGATTTTTGTATTGATGT
* * * * * ** *
75415 -AATATAAAATATTAGACTAATTATTTTTATTTTACAGATTAAATAGTATTTAAGTGGTTTGATA
1 AAATATAAATTATTAGACTATTTATTTTGATTTTACAGATTAAATCGTATTTGAGTAATTTGGTA
*
75479 AGTTTAGTTTAAATTTTATTGTTTT-ATTTTTTTA-T--TGT
66 AGTTTAGTTTAAATTTTATTGTTTTGATTTTTGTATTGATGT
* ** *
75517 AAATATAAATTAATTAGACTATTTATTTTGATTGTTA-AG--T---T-GTATTTGAATGGTTTTG
1 AAATATAAATT-ATTAGACTATTTATTTTGATT-TTACAGATTAAATCGTATTTGAGTAATTTGG
* * * * *
75575 TAAGTTTAATTTAAATTTTCGTGTAATTTTTAGTATAATTTT-TATTTTTAAATTT
64 TAAGTTTAGTTTAAATTTT-AT-T--GTTTT-G-AT--TTTTGTA---TT-GATGT
* * *
75630 AAAT-TATAATTATTAGACTATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAATTTGGT
1 AAATATA-AATTATTAGACTATTTATTTTGATTTTACAGATTAAATCGTATTTGAGTAATTTGGT
75694 AAGTTTAGTTTAAATTTTA-T-TTTT-ATTTTT-TATTGA-GT
65 AAGTTTAGTTTAAATTTTATTGTTTTGATTTTTGTATTGATGT
* * * *
75732 -AATATAAATTATTAGAATAATTATTTTTATTTTACAGATTAAATCGTATTTGAGTGATTTGGTA
1 AAATATAAATTATTAGACTATTTATTTTGATTTTACAGATTAAATCGTATTTGAGTAATTTGGTA
* * *
75796 AGTTTAGTTTAAATTTTATTGTTTTGTTTTTTGTTTTTATTGT
66 AGTTTAGTTTAAATTTTATTGTTTTGATTTTTGTATTGA-TGT
75839 AAATATAAATTCATTAGACTATTTATTTTGATTTTACAGATT
1 AAATATAAATT-ATTAGACTATTTATTTTGATTTTACAGATT
75881 TTTTTGTTTA
Statistics
Matches: 468, Mismatches: 56, Indels: 96
0.75 0.09 0.15
Matches are distributed among these distances:
98 31 0.07
99 2 0.00
100 51 0.11
101 90 0.19
102 19 0.04
103 23 0.05
104 30 0.06
105 13 0.03
106 2 0.00
107 12 0.03
108 11 0.02
109 29 0.06
110 1 0.00
111 7 0.01
112 28 0.06
113 10 0.02
114 2 0.00
115 1 0.00
116 14 0.03
117 61 0.13
118 31 0.07
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (107 bp):
AAATATAAATTATTAGACTATTTATTTTGATTTTACAGATTAAATCGTATTTGAGTAATTTGGTA
AGTTTAGTTTAAATTTTATTGTTTTGATTTTTGTATTGATGT
Found at i:75763 original size:317 final size:315
Alignment explanation
Indices: 75139--75871 Score: 1045
Period size: 317 Copynumber: 2.3 Consensus size: 315
75129 AGTGGTCTGG
* * * * *
75139 TAAGCGATTTGATAAATTTAGTATAAATTTTATTGTTTCATTTTTAATTTTTTTTTGAAATATAA
1 TAAGTGATTTGATAAGTTTAGTTTAAATTTTATTGTTT--TTTTT--TTTTATTGT-AAATATAA
* * * *
75204 ATTAATTATATTATTTATTTTGATTTTACATATTAAATTGTATTGGAGTTGTTTGGTAAGTTTAA
61 ATTAATTAGACTATTTATTTTGA---T---TATTAAATTGTATTGGAATGGTTTGGTAAGTTTAA
*
75269 TTTAAATTTTCGTGTAATTTTTAGAATACTTTTATTTTTAATTTAAATTATAATTATTATACTAT
120 TTTAAATTTTCGTGTAATTTTTAGAATACTTTTATTTTTAATTTAAATTATAATTATTAGACTAT
*
75334 TTATTTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTTAGTAAGTTTAGTTTAAATTATATT
185 TTATTTTTGATTTTACATATTAAGTTGTATTTGAGTAATTTAGTAAGTTTAGTTTAAATTATATT
*
75399 TTTATTTTTATTGAGTAATATAAAATATTAGACTAATTATTTTTATTTTACAGATTAAATAGTAT
250 TTTATTTTTATTGAGTAATATAAAATATTAGAATAATTATTTTTATTTTACAGATTAAATAGTAT
75464 T
315 T
* *
75465 TAAGTGGTTTGATAAGTTTAGTTTAAATTTTATTGTTTTATTTTTTTATTGTAAATATAAATTAA
1 TAAGTGATTTGATAAGTTTAGTTTAAATTTTATTGTTTTTTTTTTTTATTGTAAATATAAATTAA
* * * *
75530 TTAGACTATTTATTTTGATTGTTAAGTTGTATTTGAATGGTTTTGTAAGTTTAATTTAAATTTTC
66 TTAGACTATTTATTTTGATTATTAAATTGTATTGGAATGGTTTGGTAAGTTTAATTTAAATTTTC
* *
75595 GTGTAATTTTTAGTATAATTTTTATTTTTAAATTTAAATTATAATTATTAGACTATTTA-TTTTG
131 GTGTAATTTTTAGAAT-ACTTTTATTTTT-AATTTAAATTATAATTATTAGACTATTTATTTTTG
* *
75659 ATTTTACATATTAAGTTGTATTTGAGTAATTTGGTAAGTTTAGTTTAAATTTTATTTTTATTTTT
194 ATTTTACATATTAAGTTGTATTTGAGTAATTTAGTAAGTTTAGTTTAAATTATATTTTTA-TTTT
* *
75724 TATTGAGTAATATAAATTATTAGAATAATTATTTTTATTTTACAGATTAAATCGTATT
258 TATTGAGTAATATAAAATATTAGAATAATTATTTTTATTTTACAGATTAAATAGTATT
* *
75782 TGAGTGATTTGGTAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTTGTTTTTATTGTAAATATAA
1 TAAGTGATTTGATAAGTTTAGTTTAAATTTTATTG---T-TTTTTT-TTTTTATTGTAAATATAA
*
75847 ATTCATTAGACTATTTATTTTGATT
61 ATTAATTAGACTATTTATTTTGATT
75872 TTACAGATTT
Statistics
Matches: 370, Mismatches: 29, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
315 55 0.15
316 73 0.20
317 119 0.32
318 1 0.00
320 1 0.00
321 34 0.09
322 49 0.13
324 4 0.01
326 34 0.09
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (315 bp):
TAAGTGATTTGATAAGTTTAGTTTAAATTTTATTGTTTTTTTTTTTTATTGTAAATATAAATTAA
TTAGACTATTTATTTTGATTATTAAATTGTATTGGAATGGTTTGGTAAGTTTAATTTAAATTTTC
GTGTAATTTTTAGAATACTTTTATTTTTAATTTAAATTATAATTATTAGACTATTTATTTTTGAT
TTTACATATTAAGTTGTATTTGAGTAATTTAGTAAGTTTAGTTTAAATTATATTTTTATTTTTAT
TGAGTAATATAAAATATTAGAATAATTATTTTTATTTTACAGATTAAATAGTATT
Found at i:75835 original size:216 final size:207
Alignment explanation
Indices: 75402--75880 Score: 490
Period size: 216 Copynumber: 2.3 Consensus size: 207
75392 TTATATTTTT
* * *
75402 ATTTTTATTG-AGTAATATAAAATATTAGACTAATTATTTTTATTTTACAGATTAAATAGTATTT
1 ATTTTTATTGTA--AATATAAATTATTAGACTATTTATTTTGATTTTACAGATTAAATAGTATTT
**
75466 AAGTGGTTTGATAAGTTTAGTTTAAATTTTATTGTTTTATTTTTTTATTGTAAATATAAATTAAT
64 AAGTAATTTGATAAGTTTAGTTTAAATTTTATTGTTTTATTTTTTTATTGTAAATATAAATTAAT
* * * * *
75531 TAGACTATTTATTTTGATTGTTAAGTTGTATTTGAATGGTTTTGTAAGTTTAATTTAAATTTTCG
129 TAGAATAATTATTTTGATTGTTAAGTTGTATTTGAATGATTTGGTAAGTTTAATTTAAATTTTAG
75596 TGTAATTTTTAGTATA
194 TGT-ATTTTTA-TATA
* * * *
75612 ATTTTTATTTTTAAATTTAAATTATAATTATTAGACTATTTATTTTGATTTTACATATTAAGTTG
1 ATTTTTA-TTGTAAA--T--A-TA-AATTATTAGACTATTTATTTTGATTTTACAGATTAAATAG
* *
75677 TATTTGAGTAATTTGGTAAGTTTAGTTTAAATTTTA-T-TTTTA-TTTTTTATTG-AGTAATATA
59 TATTTAAGTAATTTGATAAGTTTAGTTTAAATTTTATTGTTTTATTTTTTTATTGTA--AATATA
* *
75738 AATT-ATTAGAATAATTATTTTTATT-TTACAGATTAAATCGTATTTGAGTGATTTGGTAAGTTT
122 AATTAATTAGAATAATTATTTTGATTGTTA-AG--T---T-GTATTTGAATGATTTGGTAAGTTT
* * * *
75801 AGTTTAAATTTTATTGT-TTTGTT-TTTT
180 AATTTAAATTTTAGTGTATTT-TTATATA
*
75828 GTTTTTATTGTAAATATAAATTCATTAGACTATTTATTTTGATTTTACAGATT
1 ATTTTTATTGTAAATATAAATT-ATTAGACTATTTATTTTGATTTTACAGATT
75881 TTTTTGTTTA
Statistics
Matches: 225, Mismatches: 25, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
209 4 0.02
210 40 0.18
211 3 0.01
212 6 0.03
213 31 0.14
214 16 0.07
215 10 0.04
216 74 0.33
217 3 0.01
218 3 0.01
219 35 0.16
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (207 bp):
ATTTTTATTGTAAATATAAATTATTAGACTATTTATTTTGATTTTACAGATTAAATAGTATTTAA
GTAATTTGATAAGTTTAGTTTAAATTTTATTGTTTTATTTTTTTATTGTAAATATAAATTAATTA
GAATAATTATTTTGATTGTTAAGTTGTATTTGAATGATTTGGTAAGTTTAATTTAAATTTTAGTG
TATTTTTATATA
Found at i:77946 original size:23 final size:23
Alignment explanation
Indices: 77916--77986 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 23
77906 ATATTAAATA
*
77916 AAATATTGATATTATTCACATAG
1 AAATATTGATATTAATCACATAG
* *
77939 AAATATTGATTTTAATCACATTCATTC
1 AAATATTGATATTAATCACA-T-A--G
*
77966 AAATATTGGTATTAATCACAT
1 AAATATTGATATTAATCACAT
77987 TCATTCAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
23 18 0.46
24 1 0.03
25 1 0.03
26 1 0.03
27 18 0.46
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATATTGATATTAATCACATAG
Found at i:77970 original size:27 final size:27
Alignment explanation
Indices: 77916--77998 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
77906 ATATTAAATA
* *
77916 AAATATTGATATTATTCACA-T-A--G
1 AAATATTGATATTAATCACATTCATTC
*
77939 AAATATTGATTTTAATCACATTCATTC
1 AAATATTGATATTAATCACATTCATTC
*
77966 AAATATTGGTATTAATCACATTCATTC
1 AAATATTGATATTAATCACATTCATTC
77993 AAATAT
1 AAATAT
77999 AACATCAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
23 18 0.35
24 1 0.02
25 1 0.02
27 31 0.61
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (27 bp):
AAATATTGATATTAATCACATTCATTC
Found at i:80726 original size:16 final size:16
Alignment explanation
Indices: 80705--80743 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
80695 AATTTGTGAC
80705 ATATTAGATTAAAATT
1 ATATTAGATTAAAATT
*
80721 ATATTAGATTAAAGTT
1 ATATTAGATTAAAATT
80737 ATTATTA
1 A-TATTA
80744 TTATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (16 bp):
ATATTAGATTAAAATT
Found at i:80868 original size:43 final size:43
Alignment explanation
Indices: 80771--80891 Score: 170
Period size: 43 Copynumber: 2.7 Consensus size: 43
80761 AAAATAATTG
* * * *
80771 TTTTTAACATTTTTACCACAAATACTAAATCAATATTATTTTAATA
1 TTTTTAACATTTTTACTAGAAATACTAAATC---ACTATTTTAACA
*
80817 TTTTTAACATTTTTACTGGAAATACTAAATCACTATTTTAACA
1 TTTTTAACATTTTTACTAGAAATACTAAATCACTATTTTAACA
80860 TTTTTAACATTTTTACTAGAAATACTAAATCA
1 TTTTTAACATTTTTACTAGAAATACTAAATCA
80892 AATGTTGATC
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
43 41 0.59
46 28 0.41
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (43 bp):
TTTTTAACATTTTTACTAGAAATACTAAATCACTATTTTAACA
Found at i:81158 original size:24 final size:25
Alignment explanation
Indices: 81101--81160 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 25
81091 TTATTAAAGT
*
81101 TATTATTTTTCGTCATTATAATAAA
1 TATTTTTTTTCGTCATTATAATAAA
*
81126 TATTATTTTTTTCGTCATTATAAT-TA
1 TA-T-TTTTTTTCGTCATTATAATAAA
81152 TATTTTTTT
1 TATTTTTTT
81161 AATTATCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
24 6 0.19
25 3 0.10
26 4 0.13
27 18 0.58
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (25 bp):
TATTTTTTTTCGTCATTATAATAAA
Found at i:81839 original size:39 final size:39
Alignment explanation
Indices: 81785--81888 Score: 136
Period size: 39 Copynumber: 2.7 Consensus size: 39
81775 GCATGGCCTA
*
81785 AAGACGTCGTGCACTCTTGGAGTCTTATACATTGACCTG
1 AAGACGTCGTGCACTCCTGGAGTCTTATACATTGACCTG
* * * *
81824 AAGACGCCGTGCACTCCTGGAGTTTTATCCATTGGCCTG
1 AAGACGTCGTGCACTCCTGGAGTCTTATACATTGACCTG
* * *
81863 AAAACGTCATACACTCCTGGAGTCTT
1 AAGACGTCGTGCACTCCTGGAGTCTT
81889 TAAATTTAGC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (39 bp):
AAGACGTCGTGCACTCCTGGAGTCTTATACATTGACCTG
Found at i:82249 original size:106 final size:106
Alignment explanation
Indices: 82064--82277 Score: 401
Period size: 106 Copynumber: 2.0 Consensus size: 106
82054 AATTAGAGTT
*
82064 TAAATGTCGATTTAAATAGTTAAATGATTTGATTGATAAAATTAAAAGATCAATATTCAAATTAG
1 TAAATGTCGAATTAAATAGTTAAATGATTTGATTGATAAAATTAAAAGATCAATATTCAAATTAG
82129 AATCTAACTATATTTAAGCATGGCTTGGCAAGCATCGATAA
66 AATCTAACTATATTTAAGCATGGCTTGGCAAGCATCGATAA
82170 TAAATGTCGAATTAAATAGTTAAATGATTTGATTGATAAAATTAAAAGATCAATATTCAAATTAG
1 TAAATGTCGAATTAAATAGTTAAATGATTTGATTGATAAAATTAAAAGATCAATATTCAAATTAG
* *
82235 AATCTAAGTATATTTAAGCATGGCTTGGCAAGCCTCGATAA
66 AATCTAACTATATTTAAGCATGGCTTGGCAAGCATCGATAA
82276 TA
1 TA
82278 TTTCAACTTA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (106 bp):
TAAATGTCGAATTAAATAGTTAAATGATTTGATTGATAAAATTAAAAGATCAATATTCAAATTAG
AATCTAACTATATTTAAGCATGGCTTGGCAAGCATCGATAA
Found at i:89560 original size:30 final size:30
Alignment explanation
Indices: 89458--89561 Score: 129
Period size: 30 Copynumber: 3.5 Consensus size: 30
89448 CTTAGGAAAA
* *
89458 TAAAAGACT-AAATAGCAAAAACAGAAATT
1 TAAAGGACTAAAATAACAAAAACAGAAATT
* * *
89487 TATAGGACTAAAACAACAAAAATAGAAATT
1 TAAAGGACTAAAATAACAAAAACAGAAATT
* * *
89517 TAAAGGATTAAAATAATAAAAACAGAAAGT
1 TAAAGGACTAAAATAACAAAAACAGAAATT
89547 TAAAGGACTAAAATA
1 TAAAGGACTAAAATA
89562 GTATTAATAG
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 7 0.11
30 55 0.89
ACGTcount: A:0.62, C:0.08, G:0.12, T:0.19
Consensus pattern (30 bp):
TAAAGGACTAAAATAACAAAAACAGAAATT
Found at i:89574 original size:30 final size:30
Alignment explanation
Indices: 89474--89588 Score: 104
Period size: 30 Copynumber: 3.8 Consensus size: 30
89464 ACTAAATAGC
* * * * *
89474 AAAAACAGAAATTTATAGGACTAAAACAAC
1 AAAAATAGAAACTTAAAGGACTAAAATAAT
* *
89504 AAAAATAGAAATTTAAAGGATTAAAATAAT
1 AAAAATAGAAACTTAAAGGACTAAAATAAT
* * *
89534 AAAAACAGAAAGTTAAAGGACTAAAATAGT
1 AAAAATAGAAACTTAAAGGACTAAAATAAT
** * *
89564 ATTAATAGAAACTAAAAGGGCTAAA
1 AAAAATAGAAACTTAAAGGACTAAA
89589 CATTAATTAC
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (30 bp):
AAAAATAGAAACTTAAAGGACTAAAATAAT
Found at i:96832 original size:3 final size:3
Alignment explanation
Indices: 96824--96873 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
96814 CATATATTTG
* *
96824 TAA TAA TAA TAA TAA TAA TTAA T-A TACA TAA TTA TAA TAA TTA -AA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TA-A TAA TAA TAA TAA TAA TAA
96869 TAA TA
1 TAA TA
96874 TTTTTGTAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 3 0.08
3 30 0.77
4 6 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:97257 original size:40 final size:41
Alignment explanation
Indices: 97160--97396 Score: 137
Period size: 40 Copynumber: 5.6 Consensus size: 41
97150 GAAGGGCGAA
* *
97160 ACACGGTTCCTACGCGATGAGGATGACTGGTTATCTAGGGGTG
1 ACACGGTTCCTACGTGATGAGGAGGACTGG-T-TCTAGGGGTG
* * * *
97203 ACACGGCTCTTACGTGATGAGGAGGTCTGG-TC-GGGGGATG
1 ACACGGTTCCTACGTGATGAGGAGGACTGGTTCTAGGGG-TG
* * * *
97243 ACACGGTTCCTACGTGATGAGGACGA-TAGGTCATCTTTAAGAAATGATA
1 ACACGGTTCCTACGTGATGAGGAGGACT-GGT--TC--T-AG---GGGTG
* *
97292 ACACGGTTCCTACGTGATGAGGACGA-TCGGTTATCAGGGGTG
1 ACACGGTTCCTACGTGATGAGGAGGACT-GGTTCT-AGGGGTG
* *
97334 ACAC-GTCTCCTACGTGATGAGAAGGTCTGG-TCT-GGGGATG
1 ACACGGT-TCCTACGTGATGAGGAGGACTGGTTCTAGGGG-TG
* *
97374 ATACGGTTCCTACGTGATAAGGA
1 ACACGGTTCCTACGTGATGAGGA
97397 ATGCATGCCT
Statistics
Matches: 151, Mismatches: 27, Indels: 35
0.71 0.13 0.16
Matches are distributed among these distances:
39 9 0.06
40 47 0.31
41 6 0.04
42 24 0.16
43 28 0.19
45 3 0.02
47 2 0.01
49 31 0.21
50 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (41 bp):
ACACGGTTCCTACGTGATGAGGAGGACTGGTTCTAGGGGTG
Found at i:97545 original size:131 final size:130
Alignment explanation
Indices: 97066--97547 Score: 508
Period size: 131 Copynumber: 3.7 Consensus size: 130
97056 GTCATCTAAA
* ** *** * *
97066 GGTGACACGACTCCTACGTGATGAGGAGATCTGGTTAGGGGATGACACAACTCATACGCGATGAA
1 GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAG
* * * * *
97131 GA-GTTCTTGCCATCTTTATGAAGGGCGA-AACACGGTTCCTACGCGATGAGGATGACTGGTTAT
66 GATG-ACATGCCATCTTTA-G--GGACGATAACACGGTTCCTACGTGATGAGGACGA-TGGTTAT
97194 CT-AGG
126 CTGA-G
* * *
97199 GGTGACACGGCTCTTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGTGATGAG
1 GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAG
* * * * ** * *
97264 GACGATAGGTCATCTTTAAGAAATGATAACACGGTTCCTACGTGATGAGGACGATCGGTTATCAG
66 GATGACATGCCATCTTT-AGGGACGATAACACGGTTCCTACGTGATGAGGACGAT-GGTTATCTG
97329 -G
129 AG
* * * * * *
97330 GGTGACACGTCTCCTACGTGATGAGAAGGTCTGGTCTGGGGATGATACGGTTCCTACGTGATAAG
1 GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAG
* *
97395 GAATG-CATGCCTTCTTTAGGGACGATAACACGGATT-CTACGTGATGAGGACGGTAGGTTATCT
66 G-ATGACATGCCATCTTTAGGGACGATAACACGG-TTCCTACGTGATGAGGACGAT-GGTTATCT
97458 GAG
128 GAG
* * *
97461 GTTGACATGACTCCTACGTGATGAGGAGGTCTAGTCGGGGGATGACACGGTTCCTACGCGATGAG
1 GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAG
97526 GATGACATGCCATCTTTAGGGA
66 GATGACATGCCATCTTTAGGGA
97548 TAATGGTTTC
Statistics
Matches: 290, Mismatches: 50, Indels: 20
0.81 0.14 0.06
Matches are distributed among these distances:
130 41 0.14
131 148 0.51
132 34 0.12
133 65 0.22
134 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.25
Consensus pattern (130 bp):
GGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAG
GATGACATGCCATCTTTAGGGACGATAACACGGTTCCTACGTGATGAGGACGATGGTTATCTGAG
Found at i:97657 original size:34 final size:32
Alignment explanation
Indices: 97619--97710 Score: 87
Period size: 32 Copynumber: 2.8 Consensus size: 32
97609 ACAAATTTCA
*
97619 TTTCAAAGGAAAC-GACTCAAAGATAGGTGTTTTG
1 TTTCAAAGGAAACAGACGCAAAGAT---TGTTTTG
* *
97653 TTTCAAGGGAAACATACGCAAAGATTGTTTTG
1 TTTCAAAGGAAACAGACGCAAAGATTGTTTTG
* * * *
97685 TTTCAAAAGAAATATACTCAAAGATT
1 TTTCAAAGGAAACAGACGCAAAGATT
97711 TTGTTTCTCA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
32 29 0.58
34 12 0.24
35 9 0.18
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (32 bp):
TTTCAAAGGAAACAGACGCAAAGATTGTTTTG
Found at i:97687 original size:32 final size:32
Alignment explanation
Indices: 97646--97727 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
97636 CAAAGATAGG
**
97646 TGTTTTGTTTCAAGGGAAACATACGCAAAGAT
1 TGTTTTGTTTCAAAAGAAACATACGCAAAGAT
* *
97678 TGTTTTGTTTCAAAAGAAATATACTCAAAGAT
1 TGTTTTGTTTCAAAAGAAACATACGCAAAGAT
*
97710 T-TTGTT-TCTCAAAAGAAA
1 TGTT-TTGTTTCAAAAGAAA
97728 TTGTCTCAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
31 13 0.30
32 31 0.70
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTTTTGTTTCAAAAGAAACATACGCAAAGAT
Found at i:97825 original size:62 final size:63
Alignment explanation
Indices: 97681--97835 Score: 165
Period size: 62 Copynumber: 2.4 Consensus size: 63
97671 CAAAGATTGT
* *
97681 TTTGTTTCAAAAGAAATATACTCAAAGATTTTGTTTCTCAAAAGAAATTGTCTCAATAGAGACAA
1 TTTGTTTCAAAAGAAACA-ACTCAAAGA-TTTGTTTCTCAAAAGAAACTGTCT--ATAGAGACAA
97746 AA
62 AA
* * *
97748 TTTATTTTC-AGAGAAACAGACTCAAAGA-TTGTTT-TTAAAAGAAACTGTCT-TGAGAGACAAA
1 TTT-GTTTCAAAAGAAACA-ACTCAAAGATTTGTTTCTCAAAAGAAACTGTCTAT-AGAGACAAA
97809 A
63 A
*
97810 TTTGTTTCAATAGAAACAACTCAAAG
1 TTTGTTTCAAAAGAAACAACTCAAAG
97836 GATACTGATA
Statistics
Matches: 77, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
61 13 0.17
62 21 0.27
64 14 0.18
65 6 0.08
67 19 0.25
68 4 0.05
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (63 bp):
TTTGTTTCAAAAGAAACAACTCAAAGATTTGTTTCTCAAAAGAAACTGTCTATAGAGACAAAA
Found at i:97942 original size:32 final size:32
Alignment explanation
Indices: 97906--97969 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
97896 TCGCATCAGG
*
97906 ATGTTGAATCCCCAAAGATGCCCCAACATTCA
1 ATGTTGAATCCCCAAAGATACCCCAACATTCA
* *
97938 ATGTTGAATCTCCAAAGATACCCCATCATTCA
1 ATGTTGAATCCCCAAAGATACCCCAACATTCA
97970 TCGTTTCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.30, G:0.11, T:0.25
Consensus pattern (32 bp):
ATGTTGAATCCCCAAAGATACCCCAACATTCA
Found at i:102464 original size:30 final size:30
Alignment explanation
Indices: 102358--102462 Score: 131
Period size: 30 Copynumber: 3.5 Consensus size: 30
102348 CTTAGTAAAA
* *
102358 TAAAGGACT-AAATAGCAAAAACAAAAATT
1 TAAAGGACTAAAATAGCAAAAATAGAAATT
* * *
102387 TATAGGACTAAAATAACAAAAATAGACATT
1 TAAAGGACTAAAATAGCAAAAATAGAAATT
* * *
102417 TAAAGGATTAAAATAGTAAAAATAGAAAGT
1 TAAAGGACTAAAATAGCAAAAATAGAAATT
102447 TAAAGGACTAAAATAG
1 TAAAGGACTAAAATAG
102463 TATTAACAGA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 8 0.13
30 55 0.87
ACGTcount: A:0.59, C:0.07, G:0.13, T:0.21
Consensus pattern (30 bp):
TAAAGGACTAAAATAGCAAAAATAGAAATT
Found at i:102474 original size:30 final size:30
Alignment explanation
Indices: 102358--102488 Score: 111
Period size: 30 Copynumber: 4.4 Consensus size: 30
102348 CTTAGTAAAA
* * *
102358 TAAAGGACT-AAATAGCAAAAACAAAAATT
1 TAAAGGACTAAAATAGTAAAAACAGAAACT
* ** * * *
102387 TATAGGACTAAAATAACAAAAATAGACATT
1 TAAAGGACTAAAATAGTAAAAACAGAAACT
* * *
102417 TAAAGGATTAAAATAGTAAAAATAGAAAGT
1 TAAAGGACTAAAATAGTAAAAACAGAAACT
**
102447 TAAAGGACTAAAATAGTATTAACAGAAACT
1 TAAAGGACTAAAATAGTAAAAACAGAAACT
* *
102477 AAAAGGGCTAAA
1 TAAAGGACTAAA
102489 CATTAATTAC
Statistics
Matches: 83, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
29 8 0.10
30 75 0.90
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.21
Consensus pattern (30 bp):
TAAAGGACTAAAATAGTAAAAACAGAAACT
Done.