Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006312.1 Hibiscus syriacus cultivar Beakdansim tig00015080_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: 111832
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:4925 original size:13 final size:13
Alignment explanation
Indices: 4907--4936 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
4897 TTTAATTACG
4907 CGAGTCGGTTTCT
1 CGAGTCGGTTTCT
4920 CGAGTCGGTTTCT
1 CGAGTCGGTTTCT
4933 CGAG
1 CGAG
4937 CCGAATCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.23, G:0.33, T:0.33
Consensus pattern (13 bp):
CGAGTCGGTTTCT
Found at i:7951 original size:15 final size:15
Alignment explanation
Indices: 7919--7952 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
7909 AGTAAGCTTA
7919 AATT-TTTTAAAAAT
1 AATTATTTTAAAAAT
7933 -ATTATTTTAAAAAT
1 AATTATTTTAAAAAT
7947 AATTAT
1 AATTAT
7953 AAACTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.17
14 10 0.56
15 5 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTATTTTAAAAAT
Found at i:8913 original size:22 final size:22
Alignment explanation
Indices: 8863--8949 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 22
8853 TAATATCTTT
* * *
8863 TATTATTATAATATAATTGATTA
1 TATTATAATATTATAAAT-ATTA
*
8886 TTTTATTAATATTA-AAATATTA
1 TATTA-TAATATTATAAATATTA
*
8908 TATTATACTATTATAAATATTA
1 TATTATAATATTATAAATATTA
*
8930 -A-TAAATATATTATAAATATT
1 TATTATA-ATATTATAAATATT
8950 TTAATAATTA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
20 3 0.06
21 21 0.40
22 16 0.30
23 7 0.13
24 6 0.11
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (22 bp):
TATTATAATATTATAAATATTA
Found at i:8941 original size:12 final size:12
Alignment explanation
Indices: 8924--8956 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
8914 ACTATTATAA
8924 ATATTAATAAAT
1 ATATTAATAAAT
8936 ATATT-ATAAAT
1 ATATTAATAAAT
*
8947 ATTTTAATAA
1 ATATTAATAA
8957 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATTAATAAAT
Found at i:13866 original size:21 final size:22
Alignment explanation
Indices: 13824--13866 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
13814 CGTTGGGGGG
*
13824 TTAATTTTGACATTATACCTTT
1 TTAATTTTGACATTATAACTTT
* *
13846 TTAA-TTTGACCTTTTAACTTT
1 TTAATTTTGACATTATAACTTT
13867 ATATACACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.56
Consensus pattern (22 bp):
TTAATTTTGACATTATAACTTT
Found at i:16276 original size:42 final size:42
Alignment explanation
Indices: 16224--16305 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
16214 TTTGAGAACA
* *
16224 AAAAACGCCGCAATAGATCAAGATTTATAGCGGCGTTTTTCC
1 AAAAACGCCGCAAAAGATCAAGATCTATAGCGGCGTTTTTCC
* *
16266 AAAAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTT
1 AAAAACGCCGCAAAAGATCAAGATCTATAGCGGCGTTTTT
16306 GGATACAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAACGCCGCAAAAGATCAAGATCTATAGCGGCGTTTTTCC
Found at i:16400 original size:43 final size:42
Alignment explanation
Indices: 16268--16429 Score: 177
Period size: 43 Copynumber: 3.8 Consensus size: 42
16258 GTTTTTCCAA
* *
16268 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTGGATAC
1 AAACACCGCAAAAGGTC-AGATCTAT-GTGGCGTTTTTGGATAC
* * *
16312 AAACGCCGTAAAAGGTCAGATCTA-GT-GCTGTTTTTGGATAT
1 AAACACCGCAAAAGGTCAGATCTATGTGGC-GTTTTTGGATAC
*
16353 AAACACCGCAAAAGGACAGATCTATTGTGGCGTTTTTGGATAC
1 AAACACCGCAAAAGGTCAGATCTA-TGTGGCGTTTTTGGATAC
* *
16396 AAACACTGCAAAAGAGT-AGATCTATAGCGGCGTT
1 AAACACCGCAAAAG-GTCAGATCTAT-GTGGCGTT
16430 ATTGAAAAAC
Statistics
Matches: 102, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
40 2 0.02
41 33 0.32
42 1 0.01
43 47 0.46
44 19 0.19
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (42 bp):
AAACACCGCAAAAGGTCAGATCTATGTGGCGTTTTTGGATAC
Found at i:17736 original size:2 final size:2
Alignment explanation
Indices: 17731--17761 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17721 CTCTCTACAT
17731 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17762 TATCGTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20253 original size:41 final size:41
Alignment explanation
Indices: 20184--20641 Score: 413
Period size: 41 Copynumber: 11.1 Consensus size: 41
20174 AGGGGCTCCA
* * * *
20184 ACTAAAGCACGAGTCTATAACGACGTTTGTATAAAAACGCC
1 ACTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * * **
20225 ACTAAA-TCATGAGTGTACAGCGGTGTTTGTA-AAAAAATCC
1 ACTAAAGT-ATGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* *
20265 ACTAAAGT-TAGAGTCTATAGCGGCGTTTGTATTAAAATGCC
1 ACTAAAGTAT-GAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * **
20306 ACTAAAGTATGAGTCTTTAGCGACGTTTACATAAAAACGCC
1 ACTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGCC
*
20347 ACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCC
1 ACTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* ** * *
20388 ACTAAAATACAACTATATAGCGGCGTTTGTATTAAAAACGCC
1 ACTAAAGTATGAGTCTATAGCGGCGTTTGTA-TAAAAACGCC
* * * *
20430 ACTAAAGAACGAGTCTTTAGCGGCGTTTGTATAAAAATGCC
1 ACTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGCC
** * *
20471 ACTAAAGTACAAGTCTATAGTGGCGTTTGTATAAAAACGTC
1 ACTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * * * *
20512 GCTAAAGTA-CAGTCTTTATCGGCGTTTGTCTTAAAAACGCC
1 ACTAAAGTATGAGTCTATAGCGGCGTTTGT-ATAAAAACGCC
* * * * * *
20553 ATTAAAGTATGAGTATTTAGCGGCGTTTGTTCTAAAAATGCT
1 ACTAAAGTATGAGTCTATAGCGGCGTTTG-TATAAAAACGCC
* * * * *
20595 GCTAAAGTA-CAGTCTTTAGCGGCTTTTGTTCTAAAAACGCC
1 ACTAAAGTATGAGTCTATAGCGGCGTTTG-TATAAAAACGCC
*
20636 GCTAAA
1 ACTAAA
20642 AATGCCGCTA
Statistics
Matches: 343, Mismatches: 65, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.00
40 47 0.14
41 227 0.66
42 67 0.20
43 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (41 bp):
ACTAAAGTATGAGTCTATAGCGGCGTTTGTATAAAAACGCC
Found at i:20456 original size:83 final size:82
Alignment explanation
Indices: 20184--20642 Score: 426
Period size: 83 Copynumber: 5.6 Consensus size: 82
20174 AGGGGCTCCA
* * * * * *
20184 ACTAAAGCACGAGTCTATAACGACGTTTGTATAAAAACGCCACT-AAAT-CATGAGTGTACAGCG
1 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACA--AGTATATAGCG
* **
20247 GTGTTTGTA-AAAAAATCC
64 GCGTTTGTATAAAAACGCC
* * * * ** * * *
20265 ACTAAAGTTA-GAGTCTATAGCGGCGTTTGTATTAAAATGCCACTAAAGTATGAGTCTTTAGCGA
1 ACTAAAG-TACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGG
**
20329 CGTTTACATAAAAACGCC
65 CGTTTGTATAAAAACGCC
* *
20347 ACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACAACTATATAGCGGC
1 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGGC
20412 GTTTGTATTAAAAACGCC
66 GTTTGTA-TAAAAACGCC
* * * * *
20430 ACTAAAGAACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAGTACAAGTCTATAGTGGC
1 ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGGC
*
20495 GTTTGTATAAAAACGTC
66 GTTTGTATAAAAACGCC
* * * * * ** *
20512 GCTAAAGTAC-AGTCTTTATCGGCGTTTGTCTTAAAAACGCCATTAAAGTATGAGTATTTAGCGG
1 ACTAAAGTACGAGTCTTTAGCGGCGTTTGT-ATAAAAACGCCACTAAAATACAAGTATATAGCGG
* * *
20576 CGTTTGTTCTAAAAATGCT
65 CGTTTG-TATAAAAACGCC
* * * *
20595 GCTAAAGTAC-AGTCTTTAGCGGCTTTTGTTCTAAAAACGCCGCTAAAA
1 ACTAAAGTACGAGTCTTTAGCGGCGTTTG-TATAAAAACGCCACTAAAA
20643 ATGCCGCTAT
Statistics
Matches: 311, Mismatches: 58, Indels: 16
0.81 0.15 0.04
Matches are distributed among these distances:
81 70 0.23
82 117 0.38
83 123 0.40
84 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (82 bp):
ACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGGC
GTTTGTATAAAAACGCC
Found at i:20476 original size:165 final size:164
Alignment explanation
Indices: 20184--20641 Score: 462
Period size: 165 Copynumber: 2.8 Consensus size: 164
20174 AGGGGCTCCA
* * * * *
20184 ACTAAAGCACGAGTCTATAACGACGTTTGTATAAAAACGCCACT-AAAT-CATGAGTGTACAGCG
1 ACTAAAGTA-GAGTCTTTAACGGCGTTTGTATAAAAACGCCACTAAAATACA--AGTATATAGCG
* * * *
20247 GTGTTTGTA--AAAAAATCCACTAAAGTTA-GAGTCTATAGCGGCGTTTGTATTAAAATGCCACT
63 GCGTTTGTATTAAAAAAGCCACTAAAG-TACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACT
** *
20309 AAAGTATGAGTCTTTAGCGACGTTTACATAAAAACGCC
127 AAAGTACAAGTCTATAGCGACGTTTACATAAAAACGCC
* *
20347 ACTAAAGTATGAGTCTTTAGCGGCGTTTGTATAAAAACGCCACTAAAATACAACTATATAGCGGC
1 ACTAAAGTA-GAGTCTTTAACGGCGTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGGC
* *
20412 GTTTGTATTAAAAACGCCACTAAAGAACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAA
65 GTTTGTATTAAAAAAGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAA
* * ** *
20477 GTACAAGTCTATAGTGGCGTTTGTATAAAAACGTC
130 GTACAAGTCTATAGCGACGTTTACATAAAAACGCC
* * * * * * ** *
20512 GCTAAAGTACAGTCTTTATCGGCGTTTGTCTTAAAAACGCCATTAAAGTATGAGTATTTAGCGGC
1 ACTAAAGTAGAGTCTTTAACGGCGTTTGT-ATAAAAACGCCACTAAAATACAAGTATATAGCGGC
* ** * * * *
20577 GTTTGT-TCTAAAAATGCTGCTAAAGTAC-AGTCTTTAGCGGCTTTTGTTCTAAAAACGCCGCTA
65 GTTTGTAT-TAAAAAAGCCACTAAAGTACGAGTCTTTAGCGGCGTTTG-TATAAAAATGCCACTA
20640 AA
128 AA
20642 AATGCCGCTA
Statistics
Matches: 247, Mismatches: 40, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
163 55 0.22
164 41 0.17
165 151 0.61
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (164 bp):
ACTAAAGTAGAGTCTTTAACGGCGTTTGTATAAAAACGCCACTAAAATACAAGTATATAGCGGCG
TTTGTATTAAAAAAGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACTAAAG
TACAAGTCTATAGCGACGTTTACATAAAAACGCC
Found at i:22210 original size:29 final size:29
Alignment explanation
Indices: 22162--22218 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
22152 CCCCAACACC
22162 CCTACAAGGTTCCCAAGCACTCCCAGCGA
1 CCTACAAGGTTCCCAAGCACTCCCAGCGA
*
22191 CCTACAAGG-TCGCCATGCACTCCCAGCG
1 CCTACAAGGTTC-CCAAGCACTCCCAGCG
22219 GCGACCAAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.25, C:0.42, G:0.19, T:0.14
Consensus pattern (29 bp):
CCTACAAGGTTCCCAAGCACTCCCAGCGA
Found at i:22256 original size:18 final size:19
Alignment explanation
Indices: 22233--22271 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
22223 CCAAGCTTCA
22233 CGTGCTCCCCT-CTGCTCC
1 CGTGCTCCCCTCCTGCTCC
22251 CGTGCTCCCCTCCTGCTCC
1 CGTGCTCCCCTCCTGCTCC
22270 CG
1 CG
22272 CTGCATGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.00, C:0.56, G:0.18, T:0.26
Consensus pattern (19 bp):
CGTGCTCCCCTCCTGCTCC
Found at i:22428 original size:33 final size:33
Alignment explanation
Indices: 22391--22457 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
22381 CAATTGTACA
*
22391 ATTATTGGTGAAATAATTGAGGCAGCCGGTGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGATGAC
22424 ATTATTGGTGAAATAATTGAGGCAGCCGATGAC
1 ATTATTGGTGAAATAATTGAGGCAGCCGATGAC
22457 A
1 A
22458 CCTAAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (33 bp):
ATTATTGGTGAAATAATTGAGGCAGCCGATGAC
Found at i:22562 original size:29 final size:27
Alignment explanation
Indices: 22502--22564 Score: 92
Period size: 26 Copynumber: 2.3 Consensus size: 27
22492 AACATAAAAC
*
22502 AAAGAAAGGGAGAAGAGATTGCAGCAG
1 AAAGAAAGGGAGAAGAAATTGCAGCAG
22529 -AAGAAAGGGAGAAGAAATTGCAGTCGAG
1 AAAGAAAGGGAGAAGAAATTGCAG-C-AG
22557 AAAGAAAG
1 AAAGAAAG
22565 AAAGGGAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 22 0.69
27 1 0.03
28 2 0.06
29 7 0.22
ACGTcount: A:0.51, C:0.06, G:0.35, T:0.08
Consensus pattern (27 bp):
AAAGAAAGGGAGAAGAAATTGCAGCAG
Found at i:22582 original size:13 final size:13
Alignment explanation
Indices: 22559--22605 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
22549 CAGTCGAGAA
22559 AGAAA-GAAAGGG
1 AGAAAGGAAAGGG
*
22571 AGAAAGGAAAGGA
1 AGAAAGGAAAGGG
*
22584 AGAAGAAGAAAGGG
1 AGAA-AGGAAAGGG
22598 AGATAAGG
1 AGA-AAGG
22606 CTCTTGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 12 0.43
15 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.02
Consensus pattern (13 bp):
AGAAAGGAAAGGG
Found at i:23085 original size:15 final size:14
Alignment explanation
Indices: 23065--23095 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
23055 GTTTATTAGC
23065 TTATTATATTATAAG
1 TTATTATATTA-AAG
23080 TTATTATATTAAAG
1 TTATTATATTAAAG
23094 TT
1 TT
23096 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:25327 original size:14 final size:14
Alignment explanation
Indices: 25308--25355 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
25298 TTCAAGTAGT
25308 AAATCATTACTATC
1 AAATCATTACTATC
25322 AAATCATTAC--T-
1 AAATCATTACTATC
*
25333 AAATCATTAATATC
1 AAATCATTACTATC
25347 AAATCATTA
1 AAATCATTA
25356 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:25335 original size:25 final size:25
Alignment explanation
Indices: 25307--25355 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
25297 GTTCAAGTAG
*
25307 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
25332 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
25356 AATATTAATA
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:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:25372 original size:22 final size:22
Alignment explanation
Indices: 25307--25377 Score: 63
Period size: 25 Copynumber: 3.1 Consensus size: 22
25297 GTTCAAGTAG
* *
25307 TAAATCATTACTATCAAATCATT
1 TAAATCATTAATATAAAATCA-T
*
25330 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATAAAATCAT
*
25354 TAAAT-ATTAATAATAAAATTAT
1 TAAATCATTAAT-ATAAAATCAT
25376 TA
1 TA
25378 TTATACTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 6 0.14
22 15 0.36
24 1 0.02
25 20 0.48
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATCATTAATATAAAATCAT
Found at i:25517 original size:60 final size:60
Alignment explanation
Indices: 25506--26190 Score: 327
Period size: 60 Copynumber: 11.0 Consensus size: 60
25496 CATTACTAAA
*
25506 TCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTAAA
1 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAA
* *
25566 TCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATTATTACT-AA
1 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAA
* * * * * *
25625 TCATTA-T-T-AAATCATT-AATATCAAATCATTAA-AT-ATTAATAATAATTTCATTATTACTA
1 TCATTACTATCAAATCATTAAATAT-TAAT-AATAATTTCATTATTACTAA--TCATTACTA--A
25684 A
60 A
*
25685 TCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTACTATCAAA
1 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAC--T-AAA
* * * * * *
25748 TCATTAAATATTAATAACAATT---TCATTATTACTAA--TCATTATTA--AATCATTAATATCA
1 TCATT-ACTATCAA-ATC-ATTAAAT-ATTAATAATAATTTCATTATTACTAATCATT-A-CT-A
25806 AA
59 AA
* * * * * * * * *
25808 TCATTAAATAT-TAAT-AAT-AAT-TTCATTATTA-TTAATCATTACTAAATCATTATTATAA
1 TCATT-ACTATCAAATCATTAAATATTAATAATAATTTCATTATTACT-AATCATTACTA-AA
* * ** * ** * * * * ** *
25866 TTTCATTATTAGTTATGTAACGAAAATATGGTTAATTGAACCAA--ACATTGTTCATTGTTCAAG
1 --TCATTACTA-TCAAATCA-TTAAATA---TTAA-T-AA-TAATTTCATTATT-ACTAATC-AT
25929 T-CGTAAA
54 TAC-TAAA
* * * * *
25936 TTATTACTATCAAATCATTACTAAATCATTAAT-ATCAAATCATTAAATCTTAATAATAAATTAT
1 TCATTACTATCAAATCA-T--TAAAT-ATTAATAAT--AAT--TT-CA--TTATTACT-AATCAT
*
26000 TATTACTAA
54 TACTA--AA
*
26009 TCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAAA
1 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAA
* * * *
26069 TTATTAATATCAAATTATTAAATATTAATAATAATTTCATTATTACTAATCATTATTAAA
1 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAA
* *
26129 TTATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATCATTACTAAA
1 TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAA
26189 TC
1 TC
26191 TTATAAATAC
Statistics
Matches: 471, Mismatches: 91, Indels: 126
0.68 0.13 0.18
Matches are distributed among these distances:
55 14 0.03
56 19 0.04
57 19 0.04
58 6 0.01
59 13 0.03
60 212 0.45
61 3 0.01
62 29 0.06
63 26 0.06
64 33 0.07
65 6 0.01
66 6 0.01
67 8 0.02
68 13 0.03
69 11 0.02
70 17 0.04
71 13 0.03
72 5 0.01
73 18 0.04
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (60 bp):
TCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAA
Found at i:25618 original size:70 final size:70
Alignment explanation
Indices: 25544--25693 Score: 282
Period size: 70 Copynumber: 2.1 Consensus size: 70
25534 TAACAATTTC
25544 ATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTAT
1 ATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTAT
25609 TACTA
66 TACTA
*
25614 ATTATTACTAATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTAT
1 ATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTAT
25679 TACTA
66 TACTA
*
25684 ATCATTACTA
1 ATTATTACTA
25694 TCAAATCATT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
70 78 1.00
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.43
Consensus pattern (70 bp):
ATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTAT
TACTA
Found at i:25619 original size:130 final size:119
Alignment explanation
Indices: 25484--25859 Score: 407
Period size: 130 Copynumber: 3.1 Consensus size: 119
25474 TAATAATTTC
*
25484 ATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTAT
1 ATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAACAATTTCATTAT
*
25549 TACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
66 TACTAATCA-T--T--A-C-----TATCAAATCATTAAATATTAATAACAATTTCATTATTACTA
* *
25614 ATTATTACTAATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTAT
1 ATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAACAATTTCATTAT
25679 TACTAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTA
66 TACTAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTA
* * * * * * *
25733 ATCATTACT-ATCAAATCATTAAAT-ATTAATAAC-AAT--TTCATTATTACT---AA--TCATT
1 ATTATTACTAATC--ATTACTAAATCATTAATATCAAATCATTAAATATTAATAACAATTTCATT
* * *
25788 ATTA--AATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTATTA
64 ATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTA
*
25842 ATCATTACTAAATCATTA
1 ATTATTACT-AATCATTA
25860 TTATAATTTC
Statistics
Matches: 228, Mismatches: 14, Indels: 29
0.84 0.05 0.11
Matches are distributed among these distances:
109 59 0.26
111 12 0.05
113 2 0.01
116 9 0.04
118 6 0.03
119 56 0.25
120 9 0.04
124 1 0.00
125 1 0.00
127 1 0.00
129 1 0.00
130 71 0.31
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (119 bp):
ATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAACAATTTCATTAT
TACTAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTA
Found at i:25687 original size:49 final size:49
Alignment explanation
Indices: 25625--25800 Score: 290
Period size: 49 Copynumber: 3.7 Consensus size: 49
25615 TTATTACTAA
*
25625 TCATTATTA--AATCATTAATATCAAATCATTAAATATTAATAATAATT
1 TCATTATTACTAATCATTAATATCAAATCATTAAATATTAATAACAATT
*
25672 TCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATT
1 TCATTATTACTAATCATTAATATCAAATCATTAAATATTAATAACAATT
*
25721 TCATTATTACTAATCATTACTATCAAATCATTAAATATTAATAACAATT
1 TCATTATTACTAATCATTAATATCAAATCATTAAATATTAATAACAATT
25770 TCATTATTACTAATCATT-AT-T-AAATCATTAA
1 TCATTATTACTAATCATTAATATCAAATCATTAA
25801 TATCAAATCA
Statistics
Matches: 124, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
46 10 0.08
47 10 0.08
48 1 0.01
49 103 0.83
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.42
Consensus pattern (49 bp):
TCATTATTACTAATCATTAATATCAAATCATTAAATATTAATAACAATT
Found at i:25712 original size:70 final size:70
Alignment explanation
Indices: 25547--25714 Score: 268
Period size: 70 Copynumber: 2.4 Consensus size: 70
25537 CAATTTCATT
* *
25547 ATTACTAATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 ATTACTAATCATCATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
*
25612 TAATT
66 TAATC
*
25617 ATTACTAATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 ATTACTAATCATCATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
25682 TAATC
66 TAATC
25687 ATTACT-ATCAAATCATTAAAT-ATTAATA
1 ATTACTAATC--ATCATTAAATCATTAATA
25715 ACAATTTCAT
Statistics
Matches: 93, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
69 3 0.03
70 81 0.87
71 9 0.10
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (70 bp):
ATTACTAATCATCATTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTAC
TAATC
Found at i:25955 original size:14 final size:14
Alignment explanation
Indices: 25933--25980 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
25923 TTCAAGTCGT
*
25933 AAATTATTACTATC
1 AAATCATTACTATC
25947 AAATCATTAC--T-
1 AAATCATTACTATC
*
25958 AAATCATTAATATC
1 AAATCATTACTATC
25972 AAATCATTA
1 AAATCATTA
25981 AATCTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:25996 original size:21 final size:22
Alignment explanation
Indices: 25932--26038 Score: 74
Period size: 25 Copynumber: 4.6 Consensus size: 22
25922 GTTCAAGTCG
* *
25932 TAAATTATTACTATCAAATCATT
1 TAAATCATTAATATCAAATCA-T
25955 ACTAAATCATTAATATCAAATCAT
1 --TAAATCATTAATATCAAATCAT
* *
25979 TAAATC-TTAATAATAAATTATTAT
1 TAAATCATTAAT-ATCAA--ATCAT
*
26003 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTAATATCAAATCAT
*
26027 TAAA-AATTAATA
1 TAAATCATTAATA
26039 ATAATTTCAT
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
21 11 0.16
22 12 0.18
24 13 0.19
25 19 0.28
26 8 0.12
27 4 0.06
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATCATTAATATCAAATCAT
Found at i:26014 original size:48 final size:49
Alignment explanation
Indices: 25952--26063 Score: 172
Period size: 48 Copynumber: 2.3 Consensus size: 49
25942 CTATCAAATC
**
25952 ATTACTAAATCATTAATATCAAATCATTAAATCTTAATAATAAATT-ATT
1 ATTACT-AATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
* *
26001 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
26050 ATTACTAATCATTA
1 ATTACTAATCATTA
26064 CTAAATTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
48 35 0.60
49 23 0.40
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (49 bp):
ATTACTAATCATTAATATCAAATCATTAAAAATTAATAATAAATTCATT
Found at i:26050 original size:36 final size:36
Alignment explanation
Indices: 26009--26077 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
25999 TTATTACTAA
26009 TCATTACTATCAAATCATTA-AAAATTAATAATAATT
1 TCATTACTA-CAAATCATTACAAAATTAATAATAATT
* * * *
26045 TCATTATTACTAATCATTACTAAATTATTAATA
1 TCATTACTACAAATCATTACAAAATTAATAATA
26078 TCAAATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 9 0.32
36 19 0.68
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (36 bp):
TCATTACTACAAATCATTACAAAATTAATAATAATT
Found at i:26062 original size:35 final size:35
Alignment explanation
Indices: 26021--26123 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 35
26011 ATTACTATCA
26021 AATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTAAAAATTAATAATAATTTCATTATTACT
* *
26056 AATCATTACTAAATT-AT--TAATATCA--A--A-T
1 AATCATTA-AAAATTAATAATAATTTCATTATTACT
*
26084 --T-ATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTAAAAATTAATAATAATTTCATTATTACT
26116 AATCATTA
1 AATCATTA
26124 TTAAATTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 24
0.64 0.06 0.30
Matches are distributed among these distances:
24 4 0.08
25 6 0.12
26 1 0.02
27 7 0.14
28 1 0.02
29 2 0.04
31 2 0.04
32 1 0.02
33 7 0.14
34 1 0.02
35 14 0.27
36 5 0.10
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.44
Consensus pattern (35 bp):
AATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:26071 original size:21 final size:21
Alignment explanation
Indices: 26047--26137 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
26037 TAATAATTTC
*
26047 ATTATTACTAATCATTACTAA
1 ATTATTACTAATCATTATTAA
*
26068 ATTATTAAT-ATCAAATTATTAA
1 ATTATTACTAATC--ATTATTAA
* **
26090 A-TATTAATAAT-A--ATTTC
1 ATTATTACTAATCATTATTAA
26107 ATTATTACTAATCATTATTAA
1 ATTATTACTAATCATTATTAA
26128 ATTATTACTA
1 ATTATTACTA
26138 TCAAATCATT
Statistics
Matches: 56, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
17 4 0.07
18 9 0.16
19 2 0.04
20 3 0.05
21 28 0.50
22 10 0.18
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTACTAATCATTATTAA
Found at i:26154 original size:21 final size:21
Alignment explanation
Indices: 25932--26155 Score: 58
Period size: 21 Copynumber: 10.4 Consensus size: 21
25922 GTTCAAGTCG
25932 TAAATTATTACTATCAAATCATT
1 TAAA-TATTACTATCAAATCA-T
*
25955 ACTAAATCATTAATATCAAATCAT
1 --TAAAT-ATTACTATCAAATCAT
* * * *
25979 TAAATCTTAATAATAAATTATTAT
1 TAAATATTACT-ATCAA--ATCAT
26003 TACTAATCATTACTATCAAATCAT
1 TA--AAT-ATTACTATCAAATCAT
* *
26027 TAAAAATTA--AT--AATAATT
1 TAAATATTACTATCAAATCA-T
* * * *
26045 TCATTATTACTAATC--ATTAC
1 TAAATATTACT-ATCAAATCAT
* *
26065 TAAATTATTAATATCAAATTAT
1 TAAA-TATTACTATCAAATCAT
*
26087 TAAATATTA--AT--AATAATT
1 TAAATATTACTATCAAATCA-T
* * *
26105 TCATTATTACTAATC--ATTAT
1 TAAATATTACT-ATCAAATCAT
26125 TAAATTATTACTATCAAATCAT
1 TAAA-TATTACTATCAAATCAT
26147 TAAATATTA
1 TAAATATTA
26156 ATAATAATTT
Statistics
Matches: 150, Mismatches: 26, Indels: 50
0.66 0.12 0.22
Matches are distributed among these distances:
17 8 0.05
18 15 0.10
19 4 0.03
20 11 0.07
21 42 0.28
22 27 0.18
24 14 0.09
25 18 0.12
26 7 0.05
27 4 0.03
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTACTATCAAATCAT
Found at i:28722 original size:28 final size:30
Alignment explanation
Indices: 28674--28735 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
28664 ATTTTTTATA
28674 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
28704 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
28732 TAAT
1 TAAT
28736 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:29185 original size:22 final size:22
Alignment explanation
Indices: 29160--29202 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
29150 GCTTGGCTAC
29160 AATCTCCCAGCTATGGATGCAG
1 AATCTCCCAGCTATGGATGCAG
29182 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATGGATGCA
29203 ACCCATGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (22 bp):
AATCTCCCAGCTATGGATGCAG
Found at i:29326 original size:29 final size:29
Alignment explanation
Indices: 29266--29348 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 29
29256 GTCGAGGCTT
* * *
29266 GGTCGCCGGGATTGCTTGGCGACCTACAA
1 GGTCGCTGGGACTGCATGGCGACCTACAA
* ***
29295 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGACTGCATGGCGACCTACAA
*
29324 GGTCGCTGGGACTACATGGCGACCT
1 GGTCGCTGGGACTGCATGGCGACCT
29349 GTGTTGGGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.16, C:0.25, G:0.37, T:0.22
Consensus pattern (29 bp):
GGTCGCTGGGACTGCATGGCGACCTACAA
Found at i:29379 original size:16 final size:16
Alignment explanation
Indices: 29358--29391 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
29348 TGTGTTGGGT
29358 GTTGGGTGCTGGGGAC
1 GTTGGGTGCTGGGGAC
29374 GTTGGGTGCTGGGGAC
1 GTTGGGTGCTGGGGAC
29390 GT
1 GT
29392 GCATGGCGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.56, T:0.26
Consensus pattern (16 bp):
GTTGGGTGCTGGGGAC
Found at i:44692 original size:19 final size:18
Alignment explanation
Indices: 44664--44835 Score: 85
Period size: 19 Copynumber: 9.6 Consensus size: 18
44654 ATTTCACTTG
*
44664 AAAAAGAAAAAATGATGA
1 AAAAAGAAAAAAAGATGA
*
44682 AAAAAGAAAAAAAGAAAGA
1 AAAAAGAAAAAAAG-ATGA
*
44701 TAAAAGAAGAAGAAA-ATGA
1 AAAAAGAA-AA-AAAGATGA
*
44720 AAAAATGAAAAAAAAATGA
1 AAAAA-GAAAAAAAGATGA
* *
44739 AAAATGATAAAAAAAATGA
1 AAAAAGA-AAAAAAGATGA
* *
44758 ATAGAAACAGAAAAA-ATGGA
1 A-A-AAAGAAAAAAAGAT-GA
**
44778 AAATGGAAGAAAAA-ATG-
1 AAAAAGAA-AAAAAGATGA
*
44795 AGAAAG--AAAAA-A-G-
1 AAAAAGAAAAAAAGATGA
*
44808 -AAAAGAAAAAATGATGA
1 AAAAAGAAAAAAAGATGA
44825 AAAAAGAAAAA
1 AAAAAGAAAAA
44836 GAAATAAAAG
Statistics
Matches: 120, Mismatches: 18, Indels: 32
0.71 0.11 0.19
Matches are distributed among these distances:
12 4 0.03
13 1 0.01
14 10 0.08
15 1 0.01
16 1 0.01
17 3 0.03
18 31 0.26
19 49 0.41
20 14 0.12
21 6 0.05
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.09
Consensus pattern (18 bp):
AAAAAGAAAAAAAGATGA
Found at i:44716 original size:22 final size:22
Alignment explanation
Indices: 44667--44741 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
44657 TCACTTGAAA
*
44667 AAGAAAA-AATGATGAAAAAAG
1 AAGAAAAGAAAGATGAAAAAAG
*
44688 AAAAAAAGAAAGAT-AAAAGAAG
1 AAGAAAAGAAAGATGAAAA-AAG
* *
44710 AAGAAAATGAAAAAATGAAAAAAA
1 AAGAAAA-G-AAAGATGAAAAAAG
44734 AATGAAAA
1 AA-GAAAA
44742 ATGATAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 10 0.23
22 14 0.33
23 1 0.02
24 9 0.21
25 9 0.21
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (22 bp):
AAGAAAAGAAAGATGAAAAAAG
Found at i:44755 original size:38 final size:36
Alignment explanation
Indices: 44662--44758 Score: 106
Period size: 38 Copynumber: 2.6 Consensus size: 36
44652 ATATTTCACT
**
44662 TGAAAAAGAAAAAATGATGAAAAAAGAAAAAAAGAA
1 TGAAAAAGAAAAAAAAATGAAAAAAGAAAAAAAGAA
* *
44698 AGATAAAAGAAGAAGAAAATGAAAAAATGAAAAAAA-AA
1 TGA-AAAAGAA-AAAAAAATGAAAAAA-GAAAAAAAGAA
44736 TGAAAAATGATAAAAAAAATGAA
1 TGAAAAA-GA-AAAAAAAATGAA
44759 TAGAAACAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
36 2 0.04
37 11 0.22
38 28 0.56
39 9 0.18
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (36 bp):
TGAAAAAGAAAAAAAAATGAAAAAAGAAAAAAAGAA
Found at i:44772 original size:38 final size:37
Alignment explanation
Indices: 44727--44829 Score: 104
Period size: 38 Copynumber: 2.7 Consensus size: 37
44717 TGAAAAAATG
*
44727 AAAAAAAAATGAAAAATGATAAAAAAAATGA-ATAGA
1 AAAAAAAAATGAAAAATGATAAAAAAAATGAGAAAGA
* *
44763 AACAGAAAAAATGGAAAATGGA-AGAAAAAATGAGAAAGA
1 AA-A-AAAAAATGAAAAAT-GATAAAAAAAATGAGAAAGA
*
44802 AAAAAGAAAA-GAAAAAATGATGAAAAAA
1 AAAAA-AAAATG-AAAAATGATAAAAAAA
44830 GAAAAAGAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
36 2 0.04
37 6 0.11
38 38 0.70
39 8 0.15
ACGTcount: A:0.73, C:0.01, G:0.17, T:0.10
Consensus pattern (37 bp):
AAAAAAAAATGAAAAATGATAAAAAAAATGAGAAAGA
Found at i:46181 original size:37 final size:38
Alignment explanation
Indices: 46128--46199 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 38
46118 AATTCAAAGT
46128 TAAGCCTTCACCGAAGAGTAGTGAAGCAAA-TCATCTA
1 TAAGCCTTCACCGAAGAGTAGTGAAGCAAACTCATCTA
*
46165 TAAGCCTTCACGGAAGAGTAGTGAAGCAAACTCAT
1 TAAGCCTTCACCGAAGAGTAGTGAAGCAAACTCAT
46200 TTGTTGAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (38 bp):
TAAGCCTTCACCGAAGAGTAGTGAAGCAAACTCATCTA
Found at i:46282 original size:55 final size:55
Alignment explanation
Indices: 46212--46647 Score: 517
Period size: 55 Copynumber: 7.9 Consensus size: 55
46202 GTTGAAGATT
* * ** *
46212 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTC
*
46267 GAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACCCGTTT-TATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTC
46322 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTC
*
46377 AAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTT-TATGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGTTC
*
46432 GAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTC
* * ** *
46487 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCATACCCGTTTTTTGAAGATTGTTC
1 GAGTTCTATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTC
* * * * * *** *
46542 GAG-TCTTATACTCCCTGAATGAATAGGGAGCAGACACGTTTACCGAAGATTTTTC
1 GAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTC
* * * **
46597 GAG-TCTTATACT-TCTTAAAAGAATAGGGAGCAAACCCGTTAT-TTGAAGATT
1 GAGTTC-TATACTCTC-TGAAGGAATAGAGAGCGGACCCGTT-TGTTGAAGATT
46648 TTTCAAGTCT
Statistics
Matches: 342, Mismatches: 30, Indels: 18
0.88 0.08 0.05
Matches are distributed among these distances:
54 6 0.02
55 331 0.97
56 5 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (55 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGTTC
Found at i:53009 original size:23 final size:23
Alignment explanation
Indices: 52979--53026 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
52969 AGGAGGCAAT
52979 AGGATTCAGTTAGATGCCTGCTA
1 AGGATTCAGTTAGATGCCTGCTA
53002 AGGATTCAGTTAGATGCCTGCTA
1 AGGATTCAGTTAGATGCCTGCTA
53025 AG
1 AG
53027 ACAGAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (23 bp):
AGGATTCAGTTAGATGCCTGCTA
Found at i:54353 original size:2 final size:2
Alignment explanation
Indices: 54346--54378 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54336 GTCAATATGT
54346 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54379 GATACTGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:58096 original size:17 final size:17
Alignment explanation
Indices: 58076--58109 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
58066 ATAGAATAAA
58076 AATTTTAATTGGTAATT
1 AATTTTAATTGGTAATT
* *
58093 AATTTTGATTGTTAATT
1 AATTTTAATTGGTAATT
58110 TGGGGTTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (17 bp):
AATTTTAATTGGTAATT
Found at i:60646 original size:31 final size:32
Alignment explanation
Indices: 60572--60656 Score: 106
Period size: 30 Copynumber: 2.8 Consensus size: 32
60562 TGGGGTAAAT
* *
60572 TTGAA-TTTTTAAAATTTTAGG-GAAGGGAAT
1 TTGAACTTTATAAAATTTTAGGAGAAGGGAAC
*
60602 TTGAAC-TTATAAAATTTTAGGAGAA-TGAAC
1 TTGAACTTTATAAAATTTTAGGAGAAGGGAAC
*
60632 TTGAACTTTATAAAATTTTAAGAGA
1 TTGAACTTTATAAAATTTTAGGAGA
60657 TAAAAATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 28 0.58
31 20 0.42
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.38
Consensus pattern (32 bp):
TTGAACTTTATAAAATTTTAGGAGAAGGGAAC
Found at i:60694 original size:22 final size:22
Alignment explanation
Indices: 60667--60713 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
60657 TAAAAATTGA
60667 TTTTTAATAGAAA-ATAT-ATAAT
1 TTTTTAA-A-AAATATATAATAAT
60689 TTTTTAAAAAATATATAATAAT
1 TTTTTAAAAAATATATAATAAT
60711 TTT
1 TTT
60714 AAAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.13
21 5 0.22
22 15 0.65
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTTAAAAAATATATAATAAT
Found at i:60699 original size:19 final size:20
Alignment explanation
Indices: 60677--60717 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
60667 TTTTTAATAG
*
60677 AAAATATATAAT-TTTTTAA
1 AAAATATATAATAATTTTAA
60696 AAAATATATAATAATTTTAA
1 AAAATATATAATAATTTTAA
60716 AA
1 AA
60718 TTTTAAGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATATATAATAATTTTAA
Found at i:62417 original size:15 final size:15
Alignment explanation
Indices: 62397--62431 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
62387 AAATGTTATT
*
62397 TTTATATTAAAAATA
1 TTTATATCAAAAATA
62412 TTTATATCAAAAATA
1 TTTATATCAAAAATA
62427 TTTAT
1 TTTAT
62432 TTTAGAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTATATCAAAAATA
Found at i:62970 original size:21 final size:20
Alignment explanation
Indices: 62946--62986 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
62936 TTCTTTAAAG
62946 TATAATATTATGAATATATTT
1 TATAATATTAT-AATATATTT
* *
62967 TATAATTTTATAATGTATTT
1 TATAATATTATAATATATTT
62987 GGGATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TATAATATTATAATATATTT
Found at i:70123 original size:20 final size:19
Alignment explanation
Indices: 70098--70148 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
70088 CCTTCATGAA
70098 GTATCGATACTC-GGGGTCTG
1 GTATCGATACTCAGGGG--TG
*
70118 GTATCGAGACTCAAGGGGTG
1 GTATCGATACTC-AGGGGTG
70138 GTATCGATACT
1 GTATCGATACT
70149 GATATTGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 23 0.85
22 4 0.15
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (19 bp):
GTATCGATACTCAGGGGTG
Found at i:70243 original size:20 final size:19
Alignment explanation
Indices: 70218--70266 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
70208 CTTCATGAAA
70218 TATCGATACTC-GGGGTCTGG
1 TATCGATACTCAGGGG--TGG
*
70238 TATCGAGACTCAAGGGGTGG
1 TATCGATACTC-AGGGGTGG
70258 TATCGATAC
1 TATCGATAC
70267 CGATGATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 21 0.84
22 4 0.16
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (19 bp):
TATCGATACTCAGGGGTGG
Found at i:70246 original size:119 final size:119
Alignment explanation
Indices: 70025--70270 Score: 420
Period size: 119 Copynumber: 2.1 Consensus size: 119
70015 TGTAACAACA
*
70025 ATACCGATACTGTTCTTCGTATAAGGTAAAAATAAGACAAATTTGAGGATGAGTATCAAAACCCC
1 ATACCGATACTGTTCTTCGTATAAGGTAAAAATAAGACAAATTTGAGGATGAATATCAAAACCCC
*
70090 TTCATGAAGTATCGATACTCGGGGTCTGGTATCGAGACTCAAGGGGTGGTATCG
66 TTCATGAAATATCGATACTCGGGGTCTGGTATCGAGACTCAAGGGGTGGTATCG
* * * * * *
70144 ATACTGATATTGTTCTTCGTATAAGGTAAAAATAAGGCAAATTTGAGGGTGAATATCGATACCCC
1 ATACCGATACTGTTCTTCGTATAAGGTAAAAATAAGACAAATTTGAGGATGAATATCAAAACCCC
70209 TTCATGAAATATCGATACTCGGGGTCTGGTATCGAGACTCAAGGGGTGGTATCG
66 TTCATGAAATATCGATACTCGGGGTCTGGTATCGAGACTCAAGGGGTGGTATCG
70263 ATACCGAT
1 ATACCGAT
70271 GATAATTTGA
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
119 118 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (119 bp):
ATACCGATACTGTTCTTCGTATAAGGTAAAAATAAGACAAATTTGAGGATGAATATCAAAACCCC
TTCATGAAATATCGATACTCGGGGTCTGGTATCGAGACTCAAGGGGTGGTATCG
Found at i:70459 original size:20 final size:19
Alignment explanation
Indices: 70405--70451 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
70395 CTAAATTTGG
*
70405 TATCAATACC-AAGGCCAA
1 TATCGATACCTAAGGCCAA
70423 TATCGATACCCTAAGGCCAA
1 TATCGATA-CCTAAGGCCAA
70443 TATCGATAC
1 TATCGATAC
70452 TGACAGGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 7 0.27
19 3 0.12
20 16 0.62
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (19 bp):
TATCGATACCTAAGGCCAA
Found at i:71801 original size:22 final size:22
Alignment explanation
Indices: 71775--71835 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
71765 TAGTTGTATA
71775 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
71797 GATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAAATATG
71819 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
71836 TAATTTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (22 bp):
GATTGATTTATTTTAAAATATG
Found at i:71895 original size:31 final size:31
Alignment explanation
Indices: 71860--71918 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
71850 AGTTGTATGT
* *
71860 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
71891 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
71919 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:72571 original size:32 final size:31
Alignment explanation
Indices: 72511--72572 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
72501 AATGGCTAAC
* **
72511 AATTTTATCAAATTATTATAAATTTATCATT
1 AATTTTATCAAACTATTATAAAACTATCATT
72542 AATTTCTATCAAACTATTATAAAACTATCAT
1 AATTT-TATCAAACTATTATAAAACTATCAT
72573 ATTTTTTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 5 0.19
32 22 0.81
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.45
Consensus pattern (31 bp):
AATTTTATCAAACTATTATAAAACTATCATT
Found at i:76653 original size:7 final size:7
Alignment explanation
Indices: 76637--76707 Score: 82
Period size: 7 Copynumber: 10.9 Consensus size: 7
76627 CACAATACAA
76637 CACA-TT
1 CACATTT
76643 CACATTT
1 CACATTT
76650 CACATTT
1 CACATTT
76657 CACA-TT
1 CACATTT
76663 CAC-TTCT
1 CACATT-T
76670 CACA-TT
1 CACATTT
76676 CACATTT
1 CACATTT
*
76683 CACA-AT
1 CACATTT
76689 CACATTT
1 CACATTT
76696 CAC-TTT
1 CACATTT
76702 CACATT
1 CACATT
76708 CCCGATATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
6 26 0.46
7 30 0.54
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (7 bp):
CACATTT
Found at i:76655 original size:13 final size:13
Alignment explanation
Indices: 76637--76707 Score: 92
Period size: 13 Copynumber: 5.5 Consensus size: 13
76627 CACAATACAA
76637 CACA-TTCACATTT
1 CACATTTCACA-TT
76650 CACATTTCACATT
1 CACATTTCACATT
76663 CAC-TTCTCACATT
1 CACATT-TCACATT
*
76676 CACATTTCACAAT
1 CACATTTCACATT
*
76689 CACATTTCACTTT
1 CACATTTCACATT
76702 CACATT
1 CACATT
76708 CCCGATATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
12 2 0.04
13 42 0.81
14 8 0.15
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (13 bp):
CACATTTCACATT
Found at i:86430 original size:25 final size:25
Alignment explanation
Indices: 86400--86449 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
86390 TGAACAGTAA
86400 TGAACAGTAACCTATTACAATACCG
1 TGAACAGTAACCTATTACAATACCG
* * *
86425 TGAACAGTAACTTGTTACAGTACCG
1 TGAACAGTAACCTATTACAATACCG
86450 ATTACACAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (25 bp):
TGAACAGTAACCTATTACAATACCG
Found at i:87088 original size:24 final size:24
Alignment explanation
Indices: 87059--87123 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
87049 ACAGCTTGTA
87059 TAAATTTGCACCGAAGTG-CCACG
1 TAAATTTGCACCGAAGTGACCACG
*
87082 TAGAATTTGTC-CCGAAG-GACCGCG
1 TA-AATTTG-CACCGAAGTGACCACG
**
87106 TAAAAATGCACCGAAGTG
1 TAAATTTGCACCGAAGTG
87124 TCACATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 1 0.03
23 13 0.38
24 19 0.56
25 1 0.03
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (24 bp):
TAAATTTGCACCGAAGTGACCACG
Found at i:88179 original size:25 final size:26
Alignment explanation
Indices: 88151--88201 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
88141 AAAAACTCAT
*
88151 CCATATC-GAAATTTCATCTA-AAAAC
1 CCATATCTCAAATTT-ATCTATAAAAC
*
88176 CCATTTCTCAAATTTATCTATAAAAC
1 CCATATCTCAAATTTATCTATAAAAC
88202 ATTTATCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.41, C:0.24, G:0.02, T:0.33
Consensus pattern (26 bp):
CCATATCTCAAATTTATCTATAAAAC
Found at i:95307 original size:33 final size:32
Alignment explanation
Indices: 95260--95324 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
95250 ACAAAGTTTA
* *
95260 CGATAATTGAAATACTTAAATACTTCCAAATT
1 CGATAATTCAAATACTTAAAAACTTCCAAATT
*
95292 CGATAAATTCAAATACTTAAAAACTTCCGAATT
1 CGAT-AATTCAAATACTTAAAAACTTCCAAATT
95325 TTTTAAACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (32 bp):
CGATAATTCAAATACTTAAAAACTTCCAAATT
Found at i:95812 original size:27 final size:26
Alignment explanation
Indices: 95769--95828 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
95759 ACTTTGAAGA
* * *
95769 GTATTTTTCTAACAAATCTATTA-GGG
1 GTATTTTTCAAAAAAAT-AATTATGGG
95795 GTATTTTTCAAGAAAAATAATTATGGG
1 GTATTTTTCAA-AAAAATAATTATGGG
95822 GT-TTTTT
1 GTATTTTT
95829 AATATAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.45
Consensus pattern (26 bp):
GTATTTTTCAAAAAAATAATTATGGG
Found at i:104132 original size:13 final size:13
Alignment explanation
Indices: 104114--104155 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
104104 AACGGTCAAC
104114 GGTCAACGGGTCG
1 GGTCAACGGGTCG
104127 GGTCAAC-GGTCG
1 GGTCAACGGGTCG
*
104139 GGTAAACGGGTCG
1 GGTCAACGGGTCG
104152 GGTC
1 GGTC
104156 GGGTAAACTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:104157 original size:18 final size:18
Alignment explanation
Indices: 104134--104185 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
104124 TCGGGTCAAC
104134 GGTCGGGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCG
*
104152 GGTCGGGTAAACTGGTCG
1 GGTCGGGTAAACGGGTCG
104170 GGTCGGGTAAACGGGT
1 GGTCGGGTAAACGGGT
104186 AAACGGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.15, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCG
Found at i:104185 original size:13 final size:13
Alignment explanation
Indices: 104118--104154 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
104108 GTCAACGGTC
*
104118 AACGGGTCGGGTC
1 AACGGGTCGGGTA
104131 AAC-GGTCGGGTA
1 AACGGGTCGGGTA
104143 AACGGGTCGGGT
1 AACGGGTCGGGT
104155 CGGGTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:104228 original size:11 final size:10
Alignment explanation
Indices: 104198--104249 Score: 72
Period size: 9 Copynumber: 5.3 Consensus size: 10
104188 ACGGGTCGTG
104198 ACCGGTC-AA
1 ACCGGTCAAA
104207 ACCGGTCAAA
1 ACCGGTCAAA
104217 ACCGGTTCAAA
1 ACCGG-TCAAA
*
104228 ACCGGT-TAA
1 ACCGGTCAAA
104237 ACCGGTCAAA
1 ACCGGTCAAA
104247 ACC
1 ACC
104250 AGTTTCCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
9 15 0.39
10 13 0.34
11 10 0.26
ACGTcount: A:0.37, C:0.31, G:0.19, T:0.13
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:111337 original size:29 final size:29
Alignment explanation
Indices: 111296--111351 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
111286 ATATTATTTT
111296 TTTCGAAAAAATTACT-AAAATAGCACCCA
1 TTTCGAAAAAATT-CTCAAAATAGCACCCA
** *
111325 TTTCGAATTAATTCTCAGAATAGCACC
1 TTTCGAAAAAATTCTCAAAATAGCACC
111352 AAAACCGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.09
29 21 0.91
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (29 bp):
TTTCGAAAAAATTCTCAAAATAGCACCCA
Found at i:111444 original size:19 final size:18
Alignment explanation
Indices: 111420--111465 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
111410 TCGGGTCAAC
111420 GGTCGGGTAAAACGGGTCG
1 GGTCGGGTAAAACGGGT-G
*
111439 GGTCGGGT-AAACTGGTG
1 GGTCGGGTAAAACGGGTG
111456 GGTCGGGTAA
1 GGTCGGGTAA
111466 CGGTAACGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 9 0.36
18 8 0.32
19 8 0.32
ACGTcount: A:0.20, C:0.13, G:0.48, T:0.20
Consensus pattern (18 bp):
GGTCGGGTAAAACGGGTG
Found at i:111532 original size:11 final size:10
Alignment explanation
Indices: 111482--111529 Score: 64
Period size: 9 Copynumber: 4.9 Consensus size: 10
111472 CGGGTCGTGA
111482 CGGTC-AAAC
1 CGGTCAAAAC
111491 CGGTCAAAAC
1 CGGTCAAAAC
111501 CGGTTCAAAAC
1 CGG-TCAAAAC
*
111512 CGGT-TAAAC
1 CGGTCAAAAC
111521 CGGTCAAAA
1 CGGTCAAAA
111530 ACCAGTTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 13 0.38
10 11 0.32
11 10 0.29
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (10 bp):
CGGTCAAAAC
Found at i:111532 original size:20 final size:21
Alignment explanation
Indices: 111487--111529 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
111477 CGTGACGGTC
111487 AAACCGGTCAAAACCGGTTCA
1 AAACCGGTCAAAACCGGTTCA
*
111508 AAACCGGT-TAAACCGG-TCA
1 AAACCGGTCAAAACCGGTTCA
111527 AAA
1 AAA
111530 ACCAGTTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 7 0.33
21 8 0.38
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.14
Consensus pattern (21 bp):
AAACCGGTCAAAACCGGTTCA
Done.