Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 62 of 311
Found at i:18382487 original size:27 final size:27
Alignment explanation
Indices: 18382457--18382633 Score: 203
Period size: 27 Copynumber: 6.5 Consensus size: 27
18382447 TATTGAGTCT
* * * *
18382457 GCACACTCAGTGCTATATAATCAACTC
1 GCACACTTAGTGCTACATAGTCAAATC
* *
18382484 GCACACTTAGTGCTACGTAATCAAATC
1 GCACACTTAGTGCTACATAGTCAAATC
18382511 GCACACTTAGTGCTACATAGTCAAACTC
1 GCACACTTAGTGCTACATAGTCAAA-TC
** * *
18382539 GCACACTTAGTGCCGCATGGTCAATTC
1 GCACACTTAGTGCTACATAGTCAAATC
* **
18382566 GCACACTTAGTGC-ATCATATTCATTTC
1 GCACACTTAGTGCTA-CATAGTCAAATC
*
18382593 GCACACTTAGTGCAACATAGTCAAATC
1 GCACACTTAGTGCTACATAGTCAAATC
18382620 GCACACTTAGTGCT
1 GCACACTTAGTGCT
18382634 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
GCACACTTAGTGCTACATAGTCAAATC
Found at i:18382570 original size:82 final size:81
Alignment explanation
Indices: 18382477--18382632 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
18382467 TGCTATATAA
* *
18382477 TCAACTCGCACACTTAGTGC-TACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGC
1 TCAACTCGCACACTTAGTGCAT-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGC
18382541 ACACTTAGTGCCGCATGG
64 ACACTTAGTGCCGCATGG
* * **
18382559 TCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCAC
1 TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
18382624 ACTTAGTGC
66 ACTTAGTGC
18382633 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:18390354 original size:27 final size:27
Alignment explanation
Indices: 18390324--18390501 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
18390314 ATATTGAGTC
* * * *
18390324 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
18390351 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
18390378 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
18390406 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
18390433 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
18390460 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
18390487 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
18390502 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:18390463 original size:82 final size:81
Alignment explanation
Indices: 18390345--18390500 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
18390335 TGCTATATAA
* *
18390345 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
18390410 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
18390427 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
18390491 CACTTAGTGC
65 CACTTAGTGC
18390501 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:18397144 original size:11 final size:10
Alignment explanation
Indices: 18397112--18397214 Score: 68
Period size: 12 Copynumber: 9.6 Consensus size: 10
18397102 TGAATCCTCC
*
18397112 TATTTTTTTAT
1 TATTTTATT-T
18397123 TA-TTTATTTT
1 TATTTTA-TTT
18397133 TATTCTTATTTT
1 TATT-TTA-TTT
18397145 TATTTTATTT
1 TATTTTATTT
18397155 TATTTTATTTT
1 TATTTTA-TTT
*
18397166 TATTTTTCTTT
1 TA-TTTTATTT
18397177 TGATTTTTATTT
1 T-A-TTTTATTT
*
18397189 TCATTTCAATTT
1 T-ATTT-TATTT
18397201 TA--TTATTT
1 TATTTTATTT
18397209 TATTTT
1 TATTTT
18397215 GAAAGACATA
Statistics
Matches: 77, Mismatches: 6, Indels: 19
0.75 0.06 0.19
Matches are distributed among these distances:
8 6 0.08
9 1 0.01
10 18 0.23
11 21 0.27
12 31 0.40
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (10 bp):
TATTTTATTT
Found at i:18397152 original size:5 final size:5
Alignment explanation
Indices: 18397112--18397214 Score: 68
Period size: 5 Copynumber: 19.2 Consensus size: 5
18397102 TGAATCCTCC
*
18397112 TATTT TTTTAT TA-TT TATTTT TATTCT TATTTT TATTT TATTT TATTT
1 TATTT TATT-T TATTT TA-TTT TATT-T TA-TTT TATTT TATTT TATTT
* *
18397160 TATTTT TATTTT TCTTT TGATTTT TATTT TCATTT CAATTT TA--T TATTT
1 TA-TTT TA-TTT TATTT T-A-TTT TATTT T-ATTT -TATTT TATTT TATTT
18397209 TATTT T
1 TATTT T
18397215 GAAAGACATA
Statistics
Matches: 80, Mismatches: 6, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
3 3 0.04
4 3 0.04
5 37 0.46
6 31 0.39
7 6 0.08
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:18397152 original size:27 final size:26
Alignment explanation
Indices: 18397112--18397214 Score: 86
Period size: 27 Copynumber: 3.8 Consensus size: 26
18397102 TGAATCCTCC
18397112 TATTTTTTTATTA-TTTATTTTTATTCT
1 TATTTTTTT-TTATTTTA-TTTTATTCT
*
18397139 TATTTTTATTTTATTTTATTTTATTTT
1 TATTTTT-TTTTATTTTATTTTATTCT
18397166 TATTTTTCTTTTGATTTTTATTTTCATT-T
1 TATTTTT-TTTT-A-TTTTATTTT-ATTCT
* * *
18397195 CA-ATTTTATTATTTTATTTT
1 TATTTTTTTTTATTTTATTTT
18397215 GAAAGACATA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
25 9 0.14
26 1 0.02
27 32 0.48
28 10 0.15
29 11 0.17
30 3 0.05
ACGTcount: A:0.18, C:0.04, G:0.01, T:0.77
Consensus pattern (26 bp):
TATTTTTTTTTATTTTATTTTATTCT
Found at i:18397184 original size:7 final size:6
Alignment explanation
Indices: 18397116--18397194 Score: 92
Period size: 6 Copynumber: 13.5 Consensus size: 6
18397106 TCCTCCTATT
*
18397116 TTTTTA TTATTTA TTTTTA TTCTTA TTTTTA -TTTTA -TTTTA -TTTTA
1 TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * *
18397162 TTTTTA TTTTTC TTTTGA TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
18397195 CAATTTTATT
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
5 15 0.23
6 43 0.67
7 6 0.09
ACGTcount: A:0.16, C:0.04, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:18405304 original size:8 final size:8
Alignment explanation
Indices: 18405283--18405314 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
18405273 TTTAATAAGA
18405283 TATTTTA-
1 TATTTTAT
18405290 T-TTTTAT
1 TATTTTAT
18405297 TATTTTAT
1 TATTTTAT
18405305 TATTTTAT
1 TATTTTAT
18405313 TA
1 TA
18405315 GTATATAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
6 5 0.22
7 2 0.09
8 16 0.70
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:18407604 original size:46 final size:46
Alignment explanation
Indices: 18407112--18407570 Score: 729
Period size: 46 Copynumber: 10.0 Consensus size: 46
18407102 GTGTGCTCTT
*
18407112 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
18407158 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
* *
18407204 TGATACGAAATGTTTAAGACCATGGTTGAAAGATACCATGGTAACC
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
18407250 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
18407296 TGATACGAAATGTGTAAGACCATGGTTGAAAGTTACCATGGCAACC
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
* *
18407342 TGGTACGAAATGTGTAAGACCATGGTTGAAAGTTACCATGGCAACC
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
18407388 TGGTACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
* * *
18407434 TGATAGGAAATGTGTAAGACCATGATTGAAAGATACCATTGCAACC
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
* ** ** *
18407480 TAATATAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACG
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
* ** *
18407526 TGATATGAAATGAATAAGACCATGCTTGAAAGATACCATGGCAAC
1 TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
18407571 AAGGCAGAAA
Statistics
Matches: 390, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 390 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (46 bp):
TGATACGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
Found at i:18421808 original size:15 final size:15
Alignment explanation
Indices: 18421785--18421814 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18421775 AAACATACAT
*
18421785 CCAGGACCAAACCGA
1 CCAGAACCAAACCGA
18421800 CCAGAACCAAACCGA
1 CCAGAACCAAACCGA
18421815 TCTACCCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.40, G:0.17, T:0.00
Consensus pattern (15 bp):
CCAGAACCAAACCGA
Found at i:18421880 original size:13 final size:13
Alignment explanation
Indices: 18421862--18421889 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18421852 GGGAGTATAC
18421862 TTAACCCTTCTCT
1 TTAACCCTTCTCT
18421875 TTAACCCTTCTCT
1 TTAACCCTTCTCT
18421888 TT
1 TT
18421890 CTTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.36, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAACCCTTCTCT
Found at i:18422145 original size:145 final size:145
Alignment explanation
Indices: 18421882--18422149 Score: 446
Period size: 145 Copynumber: 1.8 Consensus size: 145
18421872 TCTTTAACCC
* * *
18421882 TTCTCTTTCTTATTTATTCTTTTATTATTACACATTGAAGGTAACGTGGGTTAAGTAGGGGGTGT
1 TTCTCTTTCTTATTTATTCTTTTATTATTACACATTGAAGGCAACGTAGGTTAAGTAGGGCGTGT
* *
18421947 TGGATTAGTAAATATGCATGATTGTTTCTCTTTCGCATTTGTTAATTCTTATGCTAGGACAAGGA
66 TGAATTAGTAAATATGCATGATTGTTTCTCTTTCACATTTGTTAATTCTTATGCTAGGACAAGGA
18422012 GAGTATACTTGACTG
131 GAGTATACTTGACTG
** * *
18422027 TTCTCTTTCTTATTTATTCTTTTATTATTACGTATTGAGGGCAATGTAGGTTAAGTAGGGCGTGT
1 TTCTCTTTCTTATTTATTCTTTTATTATTACACATTGAAGGCAACGTAGGTTAAGTAGGGCGTGT
*
18422092 TGAATTAGTAAGTATGCATGATTGTTTCTCTTTCACATTTGTTAATTCTTATGCTAGG
66 TGAATTAGTAAATATGCATGATTGTTTCTCTTTCACATTTGTTAATTCTTATGCTAGG
18422150 TTTATTCGTT
Statistics
Matches: 113, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
145 113 1.00
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.45
Consensus pattern (145 bp):
TTCTCTTTCTTATTTATTCTTTTATTATTACACATTGAAGGCAACGTAGGTTAAGTAGGGCGTGT
TGAATTAGTAAATATGCATGATTGTTTCTCTTTCACATTTGTTAATTCTTATGCTAGGACAAGGA
GAGTATACTTGACTG
Found at i:18423932 original size:6 final size:6
Alignment explanation
Indices: 18423921--18423968 Score: 78
Period size: 6 Copynumber: 8.0 Consensus size: 6
18423911 CACCGATCTT
* *
18423921 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTT CCCTTC CACTTC CCCTTC
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC CCCTTC
18423969 TCCCATCCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.02, C:0.62, G:0.00, T:0.35
Consensus pattern (6 bp):
CCCTTC
Found at i:18426543 original size:18 final size:18
Alignment explanation
Indices: 18426473--18426550 Score: 66
Period size: 18 Copynumber: 4.0 Consensus size: 18
18426463 CAATTAAACC
*
18426473 ATTTGATTGATATATTTA
1 ATTTGATTTATATATTTA
*
18426491 ATTTGATTTATTTATTTATA
1 ATTTGATTTATATA-TT-TA
*
18426511 ATTGAGTATTATTATATATTTA
1 ATT-TG-A-T-TTATATATTTA
*
18426533 ATTTGATTTATTTATTTA
1 ATTTGATTTATATATTTA
18426551 TAAATAAATC
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
18 22 0.46
19 3 0.06
20 6 0.12
21 2 0.04
22 6 0.12
23 3 0.06
24 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (18 bp):
ATTTGATTTATATATTTA
Found at i:18426631 original size:18 final size:18
Alignment explanation
Indices: 18426589--18426625 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
18426579 ACAATTTAAA
18426589 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
18426607 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
18426625 A
1 A
18426626 AGTAAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:18426752 original size:20 final size:19
Alignment explanation
Indices: 18426707--18426744 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18426697 CATCCAAACA
*
18426707 CCAGAAAAGTAAATTATTT
1 CCAGAAAAGTAAATCATTT
*
18426726 CTAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
18426745 TCCGGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:18426758 original size:14 final size:14
Alignment explanation
Indices: 18426736--18426773 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
18426726 CTAGAAAAGT
*
18426736 AAATCATTTTCCGG
1 AAATTATTTTCCGG
18426750 AAATTATTTTCCGG
1 AAATTATTTTCCGG
*
18426764 AAAATATTTT
1 AAATTATTTT
18426774 ACTGGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (14 bp):
AAATTATTTTCCGG
Found at i:18426868 original size:6 final size:6
Alignment explanation
Indices: 18426857--18426894 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
18426847 ATATGATTTG
18426857 ATTTTT ATTTTT ATTGATTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATT--TTT ATTTTT ATTTTT ATTTTT
18426895 TCTTCTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 24 0.80
8 6 0.20
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:18426882 original size:20 final size:21
Alignment explanation
Indices: 18426850--18426891 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
18426840 TTCGTGGATA
18426850 TGATTTGATTTTTATTTTTAT
1 TGATTTGATTTTTATTTTTAT
18426871 TGATTT-ATTTTTATTTTTAT
1 TGATTTGATTTTTATTTTTAT
18426891 T
1 T
18426892 TTTTCTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (21 bp):
TGATTTGATTTTTATTTTTAT
Found at i:18427486 original size:17 final size:18
Alignment explanation
Indices: 18427464--18427518 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
18427454 ACACGGGCAT
*
18427464 GCCACACA-GGTATGTGG
1 GCCACACAGGGCATGTGG
18427481 GCCACA-AGGGCATGTGG
1 GCCACACAGGGCATGTGG
* *
18427498 GCC-CACATGAGCATATGG
1 GCCACACA-GGGCATGTGG
18427516 GCC
1 GCC
18427519 CAAAATTCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.09
17 18 0.56
18 11 0.34
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.15
Consensus pattern (18 bp):
GCCACACAGGGCATGTGG
Found at i:18427511 original size:18 final size:18
Alignment explanation
Indices: 18427475--18427520 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
18427465 CCACACAGGT
*
18427475 ATGTGGG-CCACAAGGGC
1 ATGTGGGCCCACAAGAGC
*
18427492 ATGTGGGCCCACATGAGC
1 ATGTGGGCCCACAAGAGC
*
18427510 ATATGGGCCCA
1 ATGTGGGCCCA
18427521 AAATTCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (18 bp):
ATGTGGGCCCACAAGAGC
Found at i:18429097 original size:68 final size:66
Alignment explanation
Indices: 18429017--18429200 Score: 226
Period size: 68 Copynumber: 2.7 Consensus size: 66
18429007 CATCATGTGT
* *
18429017 ACAAGAAG-GCTACGAGATACTATATAGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCAT
1 ACAA-AAGAGCTACGAGAGA-TAAAT-GTAGCTAGGTCACATGTGTGATACGGGATGTATCCCAT
18429081 GTAA
63 GTAA
*
18429085 ACAAAAGAGCTACGTGAGAGATAAATGTAGCTAGGTCACATGTGTGATATGGGATGTATCCCATG
1 ACAAAAGAGCTAC--GAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATG
*
18429150 TAG
64 TAA
* * * *
18429153 ACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGATCGCATGAGTGAT
1 ACAAAAGAGCTAC--GAGAGATAAATGTAGCTAGGTCACATGTGTGAT
18429201 TCCAAGTGAA
Statistics
Matches: 105, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
67 3 0.03
68 93 0.89
69 4 0.04
70 5 0.05
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (66 bp):
ACAAAAGAGCTACGAGAGATAAATGTAGCTAGGTCACATGTGTGATACGGGATGTATCCCATGTA
A
Found at i:18435727 original size:46 final size:46
Alignment explanation
Indices: 18435676--18435844 Score: 180
Period size: 46 Copynumber: 3.6 Consensus size: 46
18435666 ATCTCATACT
* *
18435676 CGATGCATGTCCTAGACATGTCTTACACTGGCT-TACG-ACCCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CGTA-CCAAGGC
* * * *
18435722 TGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATCAATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCGTACCAAGGC
* ****
18435768 CGATGCCATGTCCCAGACATGATCTTACACTGGCTCTCATAATGTGGC
1 CGATG-CATGTCCCAGACATG-TCTTACACTGGCTCTCGTACCAAGGC
*
18435816 CGATGCATGTCCCTGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
18435845 AGCCACCAAT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
46 49 0.47
47 31 0.30
48 24 0.23
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCGTACCAAGGC
Found at i:18455024 original size:9 final size:9
Alignment explanation
Indices: 18455010--18455040 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
18455000 TAAACGAATT
18455010 GAGTTATTC
1 GAGTTATTC
*
18455019 GAGTTAATC
1 GAGTTATTC
18455028 GAGTTATTC
1 GAGTTATTC
18455037 GAGT
1 GAGT
18455041 CAACTCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.39
Consensus pattern (9 bp):
GAGTTATTC
Found at i:18457013 original size:19 final size:18
Alignment explanation
Indices: 18456989--18457029 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
18456979 ATTTTAAAAC
*
18456989 AAAATTGAATTTATTTTTA
1 AAAATTGAATTT-TATTTA
*
18457008 AAAATTTAATTTTATTTA
1 AAAATTGAATTTTATTTA
18457026 AAAA
1 AAAA
18457030 ACAATTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
AAAATTGAATTTTATTTA
Found at i:18458020 original size:24 final size:24
Alignment explanation
Indices: 18457970--18458020 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
18457960 ATCTTTATTT
* * *
18457970 TAAAAAATATTTAATATATGTATA
1 TAAAAAATATTTAAAATATGCAAA
18457994 TAAAAAATATTTACAAATAT-CAAA
1 TAAAAAATATTTA-AAATATGCAAA
18458018 TAA
1 TAA
18458021 TAAGGTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAAAAATATTTAAAATATGCAAA
Found at i:18461069 original size:17 final size:18
Alignment explanation
Indices: 18461035--18461080 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
18461025 CCGTTATGTC
18461035 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
18461050 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
18461067 CGCGACCGCGACCG
1 CGCGACCGCGACCG
18461081 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:18474315 original size:14 final size:14
Alignment explanation
Indices: 18474296--18474326 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18474286 TGCTACTATT
18474296 TTACTATTATGTTG
1 TTACTATTATGTTG
*
18474310 TTACTATTTTGTTG
1 TTACTATTATGTTG
18474324 TTA
1 TTA
18474327 TTGTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:18474397 original size:30 final size:30
Alignment explanation
Indices: 18474361--18474421 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
18474351 ATTTTATTGT
*
18474361 TAATTTTTTTATTATTTTAAAGACATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
* *
18474391 TAATTTTGTTATTATTTTAGAGGCATTTGC
1 TAATTTTGTTATTATTTTAAAGACATTTGC
18474421 T
1 T
18474422 TATTAAATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACATTTGC
Found at i:18476575 original size:40 final size:42
Alignment explanation
Indices: 18476490--18476608 Score: 131
Period size: 41 Copynumber: 2.9 Consensus size: 42
18476480 CTTGCTATCA
* * *
18476490 ATGAGCTTTAAC-CATTCACCCAAAATATGATGCTTCTACGT
1 ATGAGCTTAAACTGATTCACCCAAAATATGATGCTTCTACGC
* * *
18476531 ATGAGCTTAAATTG-TTCA-CCAAAATATGGTGC-TCTTAGGC
1 ATGAGCTTAAACTGATTCACCCAAAATATGATGCTTC-TACGC
*
18476571 ATGAGCTTAAACTGATT-ATCCAAAATATGATGCTTCTA
1 ATGAGCTTAAACTGATTCACCCAAAATATGATGCTTCTA
18476609 AGCACAAGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
39 2 0.03
40 30 0.46
41 31 0.48
42 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (42 bp):
ATGAGCTTAAACTGATTCACCCAAAATATGATGCTTCTACGC
Found at i:18479498 original size:3 final size:3
Alignment explanation
Indices: 18479490--18479518 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18479480 GCTAACTGTT
18479490 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
18479519 TTTTCCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:18482508 original size:18 final size:19
Alignment explanation
Indices: 18482471--18482508 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
18482461 TTTAATTTTA
* *
18482471 ATTTTTTAGAATTAATATT
1 ATTTTTTACAATTAAAATT
18482490 ATTTTTTACAA-TAAAATT
1 ATTTTTTACAATTAAAATT
18482508 A
1 A
18482509 ATATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTTTTACAATTAAAATT
Found at i:18483492 original size:15 final size:15
Alignment explanation
Indices: 18483474--18483503 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18483464 TTCCTCTTCT
*
18483474 TTCTTTTTCTTTTTG
1 TTCTTTTCCTTTTTG
18483489 TTCTTTTCCTTTTTG
1 TTCTTTTCCTTTTTG
18483504 CCTCCTATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.77
Consensus pattern (15 bp):
TTCTTTTCCTTTTTG
Found at i:18486627 original size:28 final size:28
Alignment explanation
Indices: 18486587--18486740 Score: 274
Period size: 28 Copynumber: 5.5 Consensus size: 28
18486577 TAAATTGTAC
18486587 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
18486615 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
18486643 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
18486671 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
18486699 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
18486726 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
18486741 GACTTAATAT
Statistics
Matches: 124, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
27 24 0.19
28 100 0.81
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.34
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:18486653 original size:56 final size:56
Alignment explanation
Indices: 18486562--18486740 Score: 279
Period size: 56 Copynumber: 3.2 Consensus size: 56
18486552 GAGATTGGCG
* * * *
18486562 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
18486619 CTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
18486675 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
*
18486730 CTGAGTGTGCG
1 CTAAGTGTGCG
18486741 GACTTAATAT
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
55 23 0.20
56 76 0.67
57 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTGATTATATAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
Found at i:18493434 original size:23 final size:23
Alignment explanation
Indices: 18493391--18493434 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
18493381 TATTTTATGT
*
18493391 AAAAGAAAGGAAATAATAAAAGA
1 AAAAGAAAGGAAAGAATAAAAGA
18493414 AAAAGAAA-GAAAGAATGAAAA
1 AAAAGAAAGGAAAGAAT-AAAA
18493435 TGTGATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (23 bp):
AAAAGAAAGGAAAGAATAAAAGA
Found at i:18494773 original size:27 final size:28
Alignment explanation
Indices: 18494688--18494785 Score: 171
Period size: 28 Copynumber: 3.5 Consensus size: 28
18494678 TAAATTGTAC
18494688 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
18494716 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
18494744 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATGT
*
18494771 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
18494786 GACTTAATAT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 23 0.34
28 45 0.66
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATGT
Found at i:18494796 original size:27 final size:27
Alignment explanation
Indices: 18494688--18494798 Score: 107
Period size: 28 Copynumber: 4.0 Consensus size: 27
18494678 TAAATTGTAC
* * *
18494688 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* * *
18494716 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
18494744 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
18494771 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
18494798 A
1 A
18494799 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 29 0.38
28 48 0.62
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:18496826 original size:21 final size:20
Alignment explanation
Indices: 18496798--18496851 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
18496788 GGAGACTCTA
18496798 AAAATTTTTCACAAAATTTC
1 AAAATTTTTCACAAAATTTC
* *
18496818 AAAATTTTTCGCGAAATTTC
1 AAAATTTTTCACAAAATTTC
18496838 AAAATTTTTC-CAAA
1 AAAATTTTTCACAAA
18496852 GTGTAGGGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.39
Consensus pattern (20 bp):
AAAATTTTTCACAAAATTTC
Found at i:18501181 original size:2 final size:2
Alignment explanation
Indices: 18501174--18501203 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18501164 ATTTCAATGT
18501174 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
18501204 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:18502241 original size:74 final size:75
Alignment explanation
Indices: 18502078--18502242 Score: 208
Period size: 75 Copynumber: 2.2 Consensus size: 75
18502068 TTATTTTGAA
* * * * ** *
18502078 GGTCACAATTATTTAATTTTTTTATGACTAAATTATTGACACTAAAATTGTAAATAATTAGGGAT
1 GGTCACAATTATTCAATTTTCTTAGGACCAAATTATTGACACTAAAATCATAAACAATTAGGGAT
18502143 GAAATTAAAT
66 GAAATTAAAT
* * * *
18502153 GGTCACAATTATTCAATTTTCTTGGGACCAAATTATTGACACTAAAATCATAAGCACTT-GTG-T
1 GGTCACAATTATTCAATTTTCTTAGGACCAAATTATTGACACTAAAATCATAAACAATTAGGGAT
18502216 CGAAATTAAAT
66 -GAAATTAAAT
18502227 GGTCACAATTATTCAA
1 GGTCACAATTATTCAA
18502243 AGAAATTGGT
Statistics
Matches: 78, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
73 1 0.01
74 28 0.36
75 49 0.63
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (75 bp):
GGTCACAATTATTCAATTTTCTTAGGACCAAATTATTGACACTAAAATCATAAACAATTAGGGAT
GAAATTAAAT
Found at i:18504556 original size:31 final size:31
Alignment explanation
Indices: 18504516--18504601 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
18504506 TCAATCTCAG
**
18504516 CATAT-ACTGGGCTGAAGCCTTTACATTATT
1 CATATCACTGGGCCAAAGCCTTTACATTATT
*
18504546 CATATCACTGGGCCAAAGCCTTTTCATTATT
1 CATATCACTGGGCCAAAGCCTTTACATTATT
*
18504577 CATATCACTGTGCCAAAGCCTTTAC
1 CATATCACTGGGCCAAAGCCTTTAC
18504602 TATAACAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (31 bp):
CATATCACTGGGCCAAAGCCTTTACATTATT
Found at i:18504852 original size:26 final size:25
Alignment explanation
Indices: 18504819--18504890 Score: 99
Period size: 26 Copynumber: 2.8 Consensus size: 25
18504809 CTCTTTTAAT
*
18504819 AACTGGGGCAAAGGCCCTTTTTGATA
1 AACTGGGGCAAA-GCCCTTTTCGATA
*
18504845 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGC-AAAGCCCTTTTCGATA
*
18504871 AATTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
18504891 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 11 0.26
26 28 0.67
27 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:18505050 original size:25 final size:25
Alignment explanation
Indices: 18505022--18505069 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
18505012 ATAATTAAAC
* **
18505022 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
18505047 CCTAGGGGCAAAACAGTCATTTT
1 CCTAGGGGCAAAACAGTCATTTT
18505070 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:18512616 original size:31 final size:31
Alignment explanation
Indices: 18512567--18512652 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
18512557 TCAATCTCAG
**
18512567 CATAT-ACTGGGCTGAAGCCTTTACATTATT
1 CATATCACTGGGCCAAAGCCTTTACATTATT
*
18512597 CATATCACTGGGCCAAAGCCTTTTCATTATT
1 CATATCACTGGGCCAAAGCCTTTACATTATT
*
18512628 CATATCACTGTGCCAAAGCCTTTAC
1 CATATCACTGGGCCAAAGCCTTTAC
18512653 TCTAACAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 5 0.10
31 45 0.90
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (31 bp):
CATATCACTGGGCCAAAGCCTTTACATTATT
Found at i:18512903 original size:26 final size:25
Alignment explanation
Indices: 18512870--18512941 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
18512860 CTCTTTTAAT
*
18512870 AACTGGGGCAAAGGCCCTTTTTGATA
1 AACTGGGGCAAA-GCCCTTTTCGATA
* *
18512896 AACTGGGGCAAAATCCCTTTTCGGTA
1 AACTGGGGC-AAAGCCCTTTTCGATA
*
18512922 AATTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
18512942 GCACTTCCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
25 10 0.25
26 27 0.68
27 3 0.08
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:18513107 original size:25 final size:25
Alignment explanation
Indices: 18513079--18513128 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
18513069 ATAATTAAAC
* **
18513079 CCTAGGGGTAAAATGGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
18513104 CCTAGGGGCAAAACAGTCATTTTTA
1 CCTAGGGGCAAAACAGTCATTTTTA
18513129 TATTATAAGG
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:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (25 bp):
CCTAGGGGCAAAACAGTCATTTTTA
Found at i:18523798 original size:68 final size:64
Alignment explanation
Indices: 18523724--18523931 Score: 195
Period size: 67 Copynumber: 3.2 Consensus size: 64
18523714 CATCATGTGT
*
18523724 ACAAGAGAGCTACAAGACATTATGACGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
1 ACAAGAGAGCTAC--GAGA-TAT-ACGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATG
18523789 TAG
62 TAG
* * * * * * *
18523792 ACAAGAGAGCTACGAGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGAGATATACGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGT
18523857 AG
63 AG
* * * * * * *
18523859 ACAAAAGAGCTACGAGATAAAC-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-G
1 ACAAGAGAGCTACGAGATATACGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
18523921 TACAAGAGAGC
1 -ACAAGAGAGC
18523932 CGAACTATAT
Statistics
Matches: 114, Mismatches: 22, Indels: 13
0.77 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.16
64 20 0.18
65 11 0.10
66 20 0.18
67 31 0.27
68 13 0.11
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.22
Consensus pattern (64 bp):
ACAAGAGAGCTACGAGATATACGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG
Found at i:18526107 original size:24 final size:25
Alignment explanation
Indices: 18526064--18526115 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
18526054 AAAAAAATTG
18526064 TATTCCATTTTCATAGTTTAT-TCA
1 TATTCCATTTTCATAGTTTATATCA
*
18526088 TATTCC-TTTTCTATATTTTATATCA
1 TATTCCATTTTC-ATAGTTTATATCA
18526113 TAT
1 TAT
18526116 CATAGTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 5 0.20
24 14 0.56
25 6 0.24
ACGTcount: A:0.25, C:0.15, G:0.02, T:0.58
Consensus pattern (25 bp):
TATTCCATTTTCATAGTTTATATCA
Found at i:18528304 original size:20 final size:20
Alignment explanation
Indices: 18528276--18528319 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
18528266 TACCAACTTG
*
18528276 CAACTTACCATAATCTTTCA
1 CAACATACCATAATCTTTCA
*
18528296 CAACATACCATAGTCTTTCA
1 CAACATACCATAATCTTTCA
18528316 CAAC
1 CAAC
18528320 TTAAACATTG
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:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (20 bp):
CAACATACCATAATCTTTCA
Found at i:18528439 original size:32 final size:33
Alignment explanation
Indices: 18528398--18528460 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
18528388 CACATAGTAC
*
18528398 CATATCAATGCC-ATATCCCAGATATGGTCTAT
1 CATATCAATGCCAATAGCCCAGATATGGTCTAT
* *
18528430 CATATCAATGCCAATAGCCTAGCTATGGTCT
1 CATATCAATGCCAATAGCCCAGATATGGTCT
18528461 TAGAAGAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (33 bp):
CATATCAATGCCAATAGCCCAGATATGGTCTAT
Found at i:18534939 original size:46 final size:46
Alignment explanation
Indices: 18534889--18535055 Score: 203
Period size: 46 Copynumber: 3.6 Consensus size: 46
18534879 CTCGTAGCCA
18534889 ATGCATGTCCCAGACATGTCTTACACTGGCT-TACGACTCGAGGCTG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCT-CGACTCGAGGCTG
* * * *
18534935 ATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCTG
1 ATGCATGTCCCAGACATGTCTTACACTGGCTCTCGACTCGAGGCTG
* * * * *
18534981 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAAT-GTGGCCG
1 ATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTC-GACTCGAGGCTG
18535029 ATGCATGTCCCAGACATGTCTTACACT
1 ATGCATGTCCCAGACATGTCTTACACT
18535056 AGCCAATAAT
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
46 53 0.51
47 27 0.26
48 22 0.21
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (46 bp):
ATGCATGTCCCAGACATGTCTTACACTGGCTCTCGACTCGAGGCTG
Found at i:18535050 original size:140 final size:141
Alignment explanation
Indices: 18534793--18535055 Score: 356
Period size: 140 Copynumber: 1.9 Consensus size: 141
18534783 GTAAGGTGCC
*
18534793 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCATATCACAAATCAATGCCATCTCCCAAACA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCACAAATCAATGCCATCTCCCAAACA
* *
18534858 TGGTCTTACAGTGACTATCATCTCGTAGCCAATGCATGTCCCAGACATGTCTTACACTGGCTTAC
66 TGGTCTTACACTGACTATCATATCGTAGCCAATGCATGTCCCAGACATGTCTTACACTGGCTTAC
18534923 GACTCGAGGCT
131 GACTCGAGGCT
* * * *
18534934 GATG-CATGTCCCAGACAT-GTCTTACACTAGCTC-TCGTCTC-AATGCTGATGCCATGTCCCAA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCTCAT-ATCACAAAT-C-AATGCCATCTCCCAA
* * * *
18534995 ACATGGTCTTACACTGGCTCTCATAAT-GTGGCCGATGCATGTCCCAGACATGTCTTACACT
63 ACATGGTCTTACACTGACTATCAT-ATCGTAGCCAATGCATGTCCCAGACATGTCTTACACT
18535056 AGCCAATAAT
Statistics
Matches: 107, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
138 4 0.04
139 18 0.17
140 80 0.75
141 5 0.05
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (141 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCTCATATCACAAATCAATGCCATCTCCCAAACA
TGGTCTTACACTGACTATCATATCGTAGCCAATGCATGTCCCAGACATGTCTTACACTGGCTTAC
GACTCGAGGCT
Found at i:18535149 original size:49 final size:49
Alignment explanation
Indices: 18535077--18535173 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 49
18535067 ACCCATAGGT
* * *
18535077 TACGGTATGAATATCCGATTTATATTCCACGTTCAAACAGGAATTCTAA
1 TACGGCATGAATATCCAATTTATATCCCACGTTCAAACAGGAATTCTAA
* *
18535126 TACGGCATGAATATTCAATTTATATCCCACGTTCAAATAGGAATTCTA
1 TACGGCATGAATATCCAATTTATATCCCACGTTCAAACAGGAATTCTA
18535174 CTATCTCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (49 bp):
TACGGCATGAATATCCAATTTATATCCCACGTTCAAACAGGAATTCTAA
Found at i:18541538 original size:24 final size:24
Alignment explanation
Indices: 18541487--18541538 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
18541477 TGTGCTTGTC
* *
18541487 TTAATGTAAATACCATAATATGTG
1 TTAATGTAAATACCATAATATATA
18541511 TTAATGTAAATACCATAAT-TCATA
1 TTAATGTAAATACCATAATAT-ATA
18541535 TTAA
1 TTAA
18541539 CTTAGTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (24 bp):
TTAATGTAAATACCATAATATATA
Found at i:18545612 original size:28 final size:28
Alignment explanation
Indices: 18545549--18545753 Score: 340
Period size: 28 Copynumber: 7.3 Consensus size: 28
18545539 ATATTAAGTC
*
18545549 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
18545576 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
18545604 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
18545632 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
18545660 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
18545688 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
18545716 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
18545745 CGCACACTT
1 CGCACACTT
18545754 TGCGCCAATC
Statistics
Matches: 169, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
27 22 0.13
28 133 0.79
29 14 0.08
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:18548953 original size:39 final size:39
Alignment explanation
Indices: 18548908--18548988 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
18548898 GCTTTACATA
18548908 CATACCTGAATCATCTTGAAATGAACTTACACATATTCT
1 CATACCTGAATCATCTTGAAATGAACTTACACATATTCT
18548947 CATACCTGAATCATCTTGAAATGAACTTACACATATTCT
1 CATACCTGAATCATCTTGAAATGAACTTACACATATTCT
18548986 CAT
1 CAT
18548989 CTTTGACATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (39 bp):
CATACCTGAATCATCTTGAAATGAACTTACACATATTCT
Found at i:18559180 original size:50 final size:50
Alignment explanation
Indices: 18559103--18559503 Score: 324
Period size: 50 Copynumber: 8.0 Consensus size: 50
18559093 TAAGATGGTT
* *
18559103 TTAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * *** * * *
18559153 TTAGGTCGCACGTGTAGTACTAAGTGCAGGCTGCTATACGTACCCGACAAC
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA-TAG
* * * * * * *
18559204 TTCA-ATCACGTGTGTAGTACTAAGTGCAAGATACTACGTATATCAGATGG
1 TT-AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* *
18559254 TTAGGTCACGTGTGTGGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * ** * *
18559304 TTAGGTCGCATGTGTAGTACTAGGTGCAGGCTACTATGCT-TACCCTACCAC
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACG-TGTACCAGA-TAG
* * * * * *
18559355 TTCA-ATCACGTGTGTAGTACTAAGTGTAGGCTACTACGGGTATCAGATGG
1 TT-AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* * * * * * *
18559405 TTAGGCCACATGTGTAGTACAAAGTGTAAGCTAATACGTGTACCGGATGG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
* ** * *
18559455 TT-GATTGCATGTGTAGTACTAAGTGCAGGCTACTATGTGTACTAGATAG
1 TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
18559504 CTTCGGTTGC
Statistics
Matches: 266, Mismatches: 77, Indels: 17
0.74 0.21 0.05
Matches are distributed among these distances:
49 37 0.14
50 158 0.59
51 69 0.26
52 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAG
Found at i:18559297 original size:101 final size:101
Alignment explanation
Indices: 18559108--18559290 Score: 258
Period size: 101 Copynumber: 1.8 Consensus size: 101
18559098 TGGTTTTAGG
* * * * *
18559108 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCACGTGTAGTAC
1 TCACGTGTGTAGTACTAAGTGCAAGATACTACGTATACCAGATAGTTAGGTCACACGTGTAGTAC
* *
18559173 TAAGTGCAGGCTGCTATACGTACCCGACAACTTCAA
66 TAAGTGCAGGCTACTACACGTACCCGACAACTTCAA
* * ** *
18559209 TCACGTGTGTAGTACTAAGTGCAAGATACTACGTATATCAGATGGTTAGGTCACGTGTGTGGTAC
1 TCACGTGTGTAGTACTAAGTGCAAGATACTACGTATACCAGATAGTTAGGTCACACGTGTAGTAC
18559274 TAAGTGCAGGCTACTAC
66 TAAGTGCAGGCTACTAC
18559291 GTGTACCAGA
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 70 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (101 bp):
TCACGTGTGTAGTACTAAGTGCAAGATACTACGTATACCAGATAGTTAGGTCACACGTGTAGTAC
TAAGTGCAGGCTACTACACGTACCCGACAACTTCAA
Found at i:18559348 original size:151 final size:151
Alignment explanation
Indices: 18559103--18559496 Score: 556
Period size: 151 Copynumber: 2.6 Consensus size: 151
18559093 TAAGATGGTT
* *
18559103 TTAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCACGTGT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
* *
18559168 AGTACTAAGTGCAGGCTGCTATACGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGTGCAA
66 AGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGTGCAA
*
18559233 GATACTACGTATATCAGATGG
131 GATACTACGGATATCAGATGG
*
18559254 TTAGGTCACGTGTGTGGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
* * * * * *
18559319 AGTACTAGGTGCAGGCTACTATGCTTACCCTACCACTTCAATCACGTGTGTAGTACTAAGTGTAG
66 AGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGTGCAA
* *
18559384 GCTACTACGGGTATCAGATGG
131 GATACTACGGATATCAGATGG
* * * * * * * * * *
18559405 TTAGGCCACATGTGTAGTACAAAGTGTAAGCTAATACGTGTACCGGATGGTT-GATTGCATGTGT
1 TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
*
18559469 AGTACTAAGTGCAGGCTACTATGTGTAC
66 AGTACTAAGTGCAGGCTACTATGCGTAC
18559497 TAGATAGCTT
Statistics
Matches: 215, Mismatches: 28, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
150 35 0.16
151 180 0.84
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (151 bp):
TTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAGTTAGGTCGCATGTGT
AGTACTAAGTGCAGGCTACTATGCGTACCCGACAACTTCAATCACGTGTGTAGTACTAAGTGCAA
GATACTACGGATATCAGATGG
Found at i:18564336 original size:27 final size:28
Alignment explanation
Indices: 18564252--18564349 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
18564242 CATGAGATTG
* * * *
18564252 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
18564281 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
18564309 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
18564336 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
18564350 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:18564360 original size:27 final size:27
Alignment explanation
Indices: 18564280--18564362 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
18564270 TAAATTGTAC
* *
18564280 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
18564308 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
18564335 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
18564362 A
1 A
18564363 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:18564363 original size:29 final size:27
Alignment explanation
Indices: 18564252--18564363 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
18564242 CATGAGATTG
** * *
18564252 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
18564281 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
18564309 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
18564336 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
18564364 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:18571488 original size:14 final size:14
Alignment explanation
Indices: 18571469--18571512 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
18571459 AATTCAAAGA
18571469 TAAAGTTAATGATT
1 TAAAGTTAATGATT
*
18571483 TAAAG-T-AT--TA
1 TAAAGTTAATGATT
18571493 TAAAGTTAATGATT
1 TAAAGTTAATGATT
18571507 TAAAGT
1 TAAAGT
18571513 ATTAGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 6 0.25
11 1 0.04
12 4 0.17
13 1 0.04
14 12 0.50
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (14 bp):
TAAAGTTAATGATT
Found at i:18571500 original size:24 final size:24
Alignment explanation
Indices: 18571468--18571524 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
18571458 CAATTCAAAG
18571468 ATAAAGTTAATGATTTAAAGTATT
1 ATAAAGTTAATGATTTAAAGTATT
18571492 ATAAAGTTAATGATTTAAAGTATT
1 ATAAAGTTAATGATTTAAAGTATT
*
18571516 AGAAA-TTAA
1 ATAAAGTTAA
18571525 AAATAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (24 bp):
ATAAAGTTAATGATTTAAAGTATT
Found at i:18573802 original size:46 final size:47
Alignment explanation
Indices: 18573699--18573871 Score: 142
Period size: 46 Copynumber: 3.7 Consensus size: 47
18573689 GGATGGTTGA
* * *
18573699 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAAT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
* * *
18573747 G--TCCAAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAA-AG
* * * ** *
18573791 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCATTTATGGATGTGAAC
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCAAAG
* * *
18573839 GC--CTGAGCTCGTTGAGTTGAATCCGAGTTCACT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
18573872 TAGGGGCGGG
Statistics
Matches: 102, Mismatches: 17, Indels: 14
0.77 0.13 0.11
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 80 0.78
47 2 0.02
48 4 0.04
49 6 0.06
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (47 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCAAAG
Found at i:18573856 original size:92 final size:92
Alignment explanation
Indices: 18573699--18573868 Score: 243
Period size: 92 Copynumber: 1.8 Consensus size: 92
18573689 GGATGGTTGA
*
18573699 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCAAACTCGTTGAGT
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCAAACTCGTTGAGT
*
18573764 TGAGTCCGAGTTCGTGAGATGTAACAG
66 TGAATCCGAGTTCGTGAGATGTAACAG
* * * ** * *
18573791 GCATCCGAACTCGTTGAGTTGAGTCTGAGTTCATTTATGGATGTGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-AAACTCGTTGAG
18573855 TTGAATCCGAGTTC
65 TTGAATCCGAGTTC
18573869 ACTTAGGGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
91 2 0.03
92 66 0.97
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (92 bp):
GCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCAAACTCGTTGAGT
TGAATCCGAGTTCGTGAGATGTAACAG
Found at i:18588920 original size:35 final size:34
Alignment explanation
Indices: 18588802--18588919 Score: 164
Period size: 34 Copynumber: 3.4 Consensus size: 34
18588792 TTGCGTCCAA
*
18588802 CGCTAGTTAGATAAACTGACGAATGTGTGCCCAG
1 CGCTAGTCAGATAAACTGACGAATGTGTGCCCAG
* *
18588836 CGCTAGTCGGATAAACTGATGAATGTGTGCCCAG
1 CGCTAGTCAGATAAACTGACGAATGTGTGCCCAG
* * * *
18588870 CACTAGTCAGCTAAATTGACGAAAGTTGTGCCCAG
1 CGCTAGTCAGATAAACTGACGAATG-TGTGCCCAG
18588905 CGCTAGTCAGATAAA
1 CGCTAGTCAGATAAA
18588920 TCAACGAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
34 50 0.69
35 22 0.31
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (34 bp):
CGCTAGTCAGATAAACTGACGAATGTGTGCCCAG
Found at i:18604002 original size:27 final size:27
Alignment explanation
Indices: 18603972--18604023 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
18603962 ATATACTTGT
*
18603972 TCTGGTGGCCTAGCCACAATATCTGTA
1 TCTGGTGACCTAGCCACAATATCTGTA
* * *
18603999 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTAGCCACAATATCTG
18604024 GCAGCCTCGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (27 bp):
TCTGGTGACCTAGCCACAATATCTGTA
Found at i:18605133 original size:16 final size:16
Alignment explanation
Indices: 18605112--18605145 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18605102 AGGCTACCGC
18605112 AAAGGAAACAAACGCA
1 AAAGGAAACAAACGCA
*
18605128 AAAGGAAACAAACTCA
1 AAAGGAAACAAACGCA
18605144 AA
1 AA
18605146 CTCAAACAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.65, C:0.18, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAGGAAACAAACGCA
Found at i:18615577 original size:27 final size:26
Alignment explanation
Indices: 18615539--18615598 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
18615529 ACATATATAT
* *
18615539 ATATTTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
18615565 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
18615592 ATATCTG
1 ATATCTG
18615599 GCAGCCTCGC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:18623207 original size:49 final size:50
Alignment explanation
Indices: 18623152--18623397 Score: 316
Period size: 49 Copynumber: 4.9 Consensus size: 50
18623142 ATCTATTGTG
*
18623152 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * *
18623202 -GGTCACATGTGTAGTACTAAGTGCATGCTACTATGAGTACCCGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT
* * * **
18623252 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
**
18623302 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
18623352 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
18623398 GCTTTGGCTA
Statistics
Matches: 166, Mismatches: 28, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
49 81 0.49
50 47 0.28
51 38 0.23
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:18623288 original size:28 final size:28
Alignment explanation
Indices: 18623257--18623340 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
18623247 AACTTCGATC
18623257 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
18623285 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
18623307 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
18623335 ACGTGT
1 ACGTGT
18623341 ACTGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:18637393 original size:27 final size:27
Alignment explanation
Indices: 18637363--18637558 Score: 257
Period size: 27 Copynumber: 7.3 Consensus size: 27
18637353 CTGAAATGCT
**
18637363 CTCGATTTGTAGAATTACCATTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
* *
18637390 CTCGATTTATAGAATTACCATTTCACC
1 CTCGATTTACAGAATTACCATTTTACC
* *
18637417 CTCGATTTACAAAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
* * *
18637444 CTCGAATTATAGAATTACAATTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
*
18637471 CTCGATTTACAGAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
*
18637498 CTCGATTTACAAAATTACCATTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
* * * *
18637525 CTCAATTTAAAAAATTACCGTTTTACC
1 CTCGATTTACAGAATTACCATTTTACC
18637552 CTCGATT
1 CTCGATT
18637559 GTGAAATTAC
Statistics
Matches: 148, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 148 1.00
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.38
Consensus pattern (27 bp):
CTCGATTTACAGAATTACCATTTTACC
Found at i:18637433 original size:54 final size:54
Alignment explanation
Indices: 18637375--18637558 Score: 287
Period size: 54 Copynumber: 3.4 Consensus size: 54
18637365 CGATTTGTAG
* *
18637375 AATTACCATTTTACCCTCGATTTATAGAATTACCATTTCACCCTCGATTTACAA
1 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAA
* * *
18637429 AATTACCGTTTTACCCTCGAATTATAGAATTACAATTTTACCCTCGATTTACAG
1 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAA
* * * *
18637483 AATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTCAATTTAAAA
1 AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAA
18637537 AATTACCGTTTTACCCTCGATT
1 AATTACCGTTTTACCCTCGATT
18637559 GTGAAATTAC
Statistics
Matches: 118, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 118 1.00
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.38
Consensus pattern (54 bp):
AATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTACAA
Found at i:18637476 original size:81 final size:81
Alignment explanation
Indices: 18637363--18637558 Score: 286
Period size: 81 Copynumber: 2.4 Consensus size: 81
18637353 CTGAAATGCT
* * *
18637363 CTCGATTTGTAGAATTACCATTTTACCCTCGATTTATAGAATTACCATTTCACCCTCGATTTACA
1 CTCGAATTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTCACCCTCGATTTACA
*
18637428 AAATTACCGTTTTACC
66 AAATTACCATTTTACC
* * *
18637444 CTCGAATTATAGAATTACAATTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACA
1 CTCGAATTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTCACCCTCGATTTACA
18637509 AAATTACCATTTTACC
66 AAATTACCATTTTACC
* * *
18637525 CTC-AATTTAAAAAATTACCGTTTTACCCTCGATT
1 CTCGAA-TTATAGAATTACCATTTTACCCTCGATT
18637559 GTGAAATTAC
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
80 2 0.02
81 101 0.98
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.38
Consensus pattern (81 bp):
CTCGAATTATAGAATTACCATTTTACCCTCGATTTACAGAATTACCATTTCACCCTCGATTTACA
AAATTACCATTTTACC
Found at i:18637620 original size:27 final size:27
Alignment explanation
Indices: 18637590--18637767 Score: 209
Period size: 27 Copynumber: 6.6 Consensus size: 27
18637580 TGTAGAATAG
*
18637590 AATTACCAAAATACCTCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
18637617 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
18637644 AATTACCAAAATACCCCTAGTTTATAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
18637671 AATTACCGAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * *
18637698 AATTATCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
* *
18637725 AATTACCAAAATACCTCT-GATTTATAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
18637752 AATTA-CAGAAATACCC
1 AATTACCA-AAATACCC
18637768 TTGACTTTCT
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
26 5 0.04
27 121 0.94
28 3 0.02
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:18637629 original size:54 final size:54
Alignment explanation
Indices: 18637557--18637767 Score: 189
Period size: 54 Copynumber: 3.9 Consensus size: 54
18637547 TTACCCTCGA
* * * *
18637557 TTGTGAAATTACTGAAATACCCCT-G-TAGAATAGAATTACCAAAATACCTCTAGT
1 TTGTAAAATTACCGAAATACCCCTAGTTAG--TAAAATTACCAAAATACCCCTAGT
* *
18637611 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGT
1 TTGTAAAATTACCGAAATACCCCTAGTTAGTAAAATTACCAAAATACCCCTAGT
* * * * * * * *
18637665 TTATAAAATTACCGAAATACCACTGGTTTGTGAAATTATCGAAATA-CCCTCAAT
1 TTGTAAAATTACCGAAATACCCCTAGTTAGTAAAATTACCAAAATACCCCT-AGT
* * *
18637719 TTGTAAAATTACCAAAATACCTCTGATTTA-TAAAATTA-CAGAAATACCC
1 TTGTAAAATTACCGAAATACCCCT-AGTTAGTAAAATTACCA-AAATACCC
18637768 TTGACTTTCT
Statistics
Matches: 129, Mismatches: 22, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
53 5 0.04
54 117 0.91
55 5 0.04
56 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (54 bp):
TTGTAAAATTACCGAAATACCCCTAGTTAGTAAAATTACCAAAATACCCCTAGT
Found at i:18637675 original size:81 final size:81
Alignment explanation
Indices: 18637590--18637766 Score: 234
Period size: 81 Copynumber: 2.2 Consensus size: 81
18637580 TGTAGAATAG
* *
18637590 AATTACCAAAATACCTCTAGTTTGTAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAA
1 AATTACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTC-AATTTGTAAAATTACCAAA
18637654 ATACCCCT-AGTTTATAA
65 ATACCCCTGA-TTTATAA
* * * * *
18637671 AATTACCGAAATACCACTGGTTTGTGAAATTATCGAAATACCCTCAATTTGTAAAATTACCAAAA
1 AATTACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAA
*
18637736 TACCTCTGATTTATAA
66 TACCCCTGATTTATAA
18637752 AATTA-CAGAAATACC
1 AATTACCA-AAATACC
18637767 CTTGACTTTC
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
80 1 0.01
81 81 0.96
82 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.31
Consensus pattern (81 bp):
AATTACCAAAATACCACTAGTTTGTAAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAA
TACCCCTGATTTATAA
Found at i:18637785 original size:29 final size:27
Alignment explanation
Indices: 18637723--18637826 Score: 95
Period size: 27 Copynumber: 3.8 Consensus size: 27
18637713 CTCAATTTGT
* *
18637723 AAAATTACCA-AAATACCTC-TGATTTAT
1 AAAATTA-CAGAAATACC-CTTGACTTAC
*
18637750 AAAATTACAGAAATACCCTTGACTTTC
1 AAAATTACAGAAATACCCTTGACTTAC
* * *
18637777 TAAAAATTATAGAAATACCATTGGCTTAC
1 --AAAATTACAGAAATACCCTTGACTTAC
*
18637806 AAAATTACTGAAATACCCTTG
1 AAAATTACAGAAATACCCTTG
18637827 GTTTGTAGAT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
26 3 0.05
27 37 0.59
29 23 0.37
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACAGAAATACCCTTGACTTAC
Found at i:18637818 original size:27 final size:28
Alignment explanation
Indices: 18637750--18637827 Score: 88
Period size: 29 Copynumber: 2.8 Consensus size: 28
18637740 TCTGATTTAT
* * *
18637750 AAAATTACAGAAATACCCTTGACTTTCTA
1 AAAATTACTGAAATACCCTTGGCTTAC-A
*
18637779 AAAATTA-TAGAAATACCATTGGCTTAC-
1 AAAATTACT-GAAATACCCTTGGCTTACA
18637806 AAAATTACTGAAATACCCTTGG
1 AAAATTACTGAAATACCCTTGG
18637828 TTTGTAGATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
27 19 0.45
28 1 0.02
29 22 0.52
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.29
Consensus pattern (28 bp):
AAAATTACTGAAATACCCTTGGCTTACA
Found at i:18637914 original size:27 final size:27
Alignment explanation
Indices: 18637871--18637944 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
18637861 AAATGACTAA
*
18637871 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
18637898 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
18637925 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
18637945 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:18637948 original size:27 final size:27
Alignment explanation
Indices: 18637884--18637948 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
18637874 ACCCCTAATA
*
18637884 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
18637911 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
18637938 GGTAAAATGAC
1 GGTAAAATGAC
18637949 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:18638795 original size:25 final size:24
Alignment explanation
Indices: 18638757--18638826 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 24
18638747 AGGAAGTGCT
*
18638757 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
18638781 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
18638806 AGAAAGGGCTTTGCCCCAGTT
1 A-AAAGGGCTTTGCCCCAGTT
18638827 ATTAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.02
25 41 0.98
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:18638839 original size:24 final size:24
Alignment explanation
Indices: 18638756--18638839 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 24
18638746 GAGGAAGTGC
* *
18638756 TAAAAGGGCTCTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
18638781 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
18638805 CAGAAAGGGCTTTGCCCCAG-TTAT
1 TA-AAAGGGCTTTGCCCCAGTTTAT
18638829 TAAAAGAGGCT
1 TAAAAG-GGCT
18638840 AGGCCTCCAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:18639033 original size:42 final size:42
Alignment explanation
Indices: 18638974--18639065 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
18638964 TAATCTCCCC
* *
18638974 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
18639016 AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
18639058 AAATGGGC
1 AAATGGGC
18639066 CTAAGGGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTAAATGTGATATTG
Found at i:18639193 original size:30 final size:31
Alignment explanation
Indices: 18639089--18639202 Score: 187
Period size: 31 Copynumber: 3.7 Consensus size: 31
18639079 CGTTTACAGT
18639089 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
18639120 AAAGGCTTCGGCCCAGTGATATGATTTGTGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
18639151 AAAGGCTTCGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
18639182 AAAGG-TTCGGCCGAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
18639203 TCAAGACTAA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
29 5 0.06
30 10 0.13
31 64 0.81
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:18649798 original size:43 final size:42
Alignment explanation
Indices: 18649748--18649846 Score: 119
Period size: 42 Copynumber: 2.3 Consensus size: 42
18649738 TCCCAGACGT
*
18649748 GGTCTTACATGTAATCAAATATCGATGC-CACTGTCCCATACAG
1 GGTCTTACATGTAATCAAATA-CGATGCTCA-TGTCCCAAACAG
* * * *
18649791 GGTCTTACATGAAATCCAATACGATGCTGATGTCCCAAACAT
1 GGTCTTACATGTAATCAAATACGATGCTCATGTCCCAAACAG
*
18649833 GGTCTTACACGTAA
1 GGTCTTACATGTAA
18649847 ATCTCAAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 28 0.58
43 20 0.42
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.27
Consensus pattern (42 bp):
GGTCTTACATGTAATCAAATACGATGCTCATGTCCCAAACAG
Found at i:18649837 original size:42 final size:43
Alignment explanation
Indices: 18649737--18649900 Score: 140
Period size: 43 Copynumber: 3.8 Consensus size: 43
18649727 CAATGGCAAC
* * *
18649737 GTCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCCACT
1 GTCCCAAACATGGTCTTACATGAAATCAAATATCGATGCCACT
* * * *
18649780 GTCCCATACAGGGTCTTACATGAAATCCAATA-CGATGCTGA-T
1 GTCCCAAACATGGTCTTACATGAAATCAAATATCGATGC-CACT
* * *
18649822 GTCCCAAACATGGTCTTACACGTAAATCTCAAAT-T-GA-GTCAAT
1 GTCCCAAACATGGTCTTACATG-AAA--TCAAATATCGATGCCACT
** *
18649865 GTCCCAAATGTGGTCTTACATGAAATCACATATCGA
1 GTCCCAAACATGGTCTTACATGAAATCAAATATCGA
18649901 AAATCCTATG
Statistics
Matches: 97, Mismatches: 16, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
40 5 0.05
41 1 0.01
42 32 0.33
43 52 0.54
44 2 0.02
45 5 0.05
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (43 bp):
GTCCCAAACATGGTCTTACATGAAATCAAATATCGATGCCACT
Found at i:18655717 original size:68 final size:67
Alignment explanation
Indices: 18655645--18655794 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
18655635 CATCATGTGT
* * * *
18655645 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
18655707 ATGTAG
62 ATGTAG
** * *
18655713 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
18655778 AG
66 AG
18655780 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
18655795 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:18655750 original size:64 final size:64
Alignment explanation
Indices: 18655669--18655852 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
18655659 AGACATTATG
* *
18655669 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
18655733 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
18655798 AA
63 AA
* * * *
18655800 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
18655853 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:18662918 original size:27 final size:27
Alignment explanation
Indices: 18662887--18663037 Score: 178
Period size: 27 Copynumber: 5.6 Consensus size: 27
18662877 TAAATTGTAC
18662887 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
18662914 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
18662940 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
18662968 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
18662996 AGCACTAAGTGTGCGATTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
18663023 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
18663038 GACTCAATAT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
27 82 0.78
28 23 0.22
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:18663001 original size:82 final size:81
Alignment explanation
Indices: 18662888--18663037 Score: 230
Period size: 82 Copynumber: 1.8 Consensus size: 81
18662878 AAATTGTACA
*
18662888 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATAT-ATAGCACTAAGTG
18662952 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** * *
18662969 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATATAGCACTGAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATATAGCACTAAGTG
18663034 TGCG
65 TGCG
18663038 GACTCAATAT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 17 0.27
82 45 0.73
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATATAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:18758895 original size:53 final size:53
Alignment explanation
Indices: 18758799--18758994 Score: 232
Period size: 53 Copynumber: 3.7 Consensus size: 53
18758789 GGATAAGTTC
* * *
18758799 TAGAATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGG
1 TAGAATTATTGAAATA-CCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGG
* *
18758853 TAGAATTATTGAAATACCCTATAGGGTAGAATTACTGAAATACCCCTGTAGGA
1 TAGAATTATTGAAATACCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGG
* * * *
18758906 TAGAATTACTGAAATACCCTTGTAGAGTAGAAATACTGAAATACCCCTGCA-GG
1 TAGAATTATTGAAATACCC-TGTAGGGTAGAATTACTGAAATACCCCTGTAGGG
** * * *
18758959 TAGAATTACCGAGATACCCTTGTGGGGTAAAATTAC
1 TAGAATTATTGAAATACCC-TGTAGGGTAGAATTAC
18758995 CATTTTGCCC
Statistics
Matches: 124, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
53 82 0.66
54 42 0.34
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (53 bp):
TAGAATTATTGAAATACCCTGTAGGGTAGAATTACTGAAATACCCCTGTAGGG
Found at i:18758936 original size:80 final size:80
Alignment explanation
Indices: 18758799--18758995 Score: 229
Period size: 80 Copynumber: 2.5 Consensus size: 80
18758789 GGATAAGTTC
* * *
18758799 TAGAATTA-TCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATT
1 TAGAATTACT-GAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGAGTAGAAATACT
*
18758863 GAAATA-CCCTATAGGG
65 GAAATACCCCTACA-GG
* *
18758879 TAGAATTACTGAAATACCCCTGT-AGGATAGAATTACTGAAATACCCTTGTAGAGTAGAAATACT
1 TAGAATTACTGAAATACCCCTGTAAGG-TAGAATTACCGAAATACCCCTGTAGAGTAGAAATACT
*
18758943 GAAATACCCCTGCAGG
65 GAAATACCCCTACAGG
* * * ** *
18758959 TAGAATTACCGAGATACCCTTGTGGGGTAAAATTACC
1 TAGAATTACTGAAATACCCCTGTAAGGTAGAATTACC
18758996 ATTTTGCCCT
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
79 3 0.03
80 89 0.89
81 8 0.08
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (80 bp):
TAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGAGTAGAAATACTG
AAATACCCCTACAGG
Found at i:18758995 original size:27 final size:27
Alignment explanation
Indices: 18758799--18758994 Score: 236
Period size: 27 Copynumber: 7.3 Consensus size: 27
18758789 GGATAAGTTC
*
18758799 TAGAATTA-TCGAAATACCCCTGTAAGG
1 TAGAATTACT-GAAATACCCCTGTAGGG
*
18758826 TAGAATTACCGAAATACCCCTGTAGGG
1 TAGAATTACTGAAATACCCCTGTAGGG
* *
18758853 TAGAATTATTGAAATA-CCCTATAGGG
1 TAGAATTACTGAAATACCCCTGTAGGG
*
18758879 TAGAATTACTGAAATACCCCTGTAGGA
1 TAGAATTACTGAAATACCCCTGTAGGG
* *
18758906 TAGAATTACTGAAATACCCTTGTAGAG
1 TAGAATTACTGAAATACCCCTGTAGGG
* *
18758933 TAGAAATACTGAAATACCCCTGCA-GG
1 TAGAATTACTGAAATACCCCTGTAGGG
* * * *
18758959 TAGAATTACCGAGATACCCTTGTGGGG
1 TAGAATTACTGAAATACCCCTGTAGGG
*
18758986 TAAAATTAC
1 TAGAATTAC
18758995 CATTTTGCCC
Statistics
Matches: 144, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
26 43 0.30
27 101 0.70
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
TAGAATTACTGAAATACCCCTGTAGGG
Found at i:18759682 original size:27 final size:26
Alignment explanation
Indices: 18759638--18759689 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
18759628 CTCGCTGTAA
*
18759638 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
18759665 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGCCACAATATCTG
18759690 GCAGCCTCGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:18765721 original size:27 final size:27
Alignment explanation
Indices: 18765683--18765882 Score: 247
Period size: 27 Copynumber: 7.4 Consensus size: 27
18765673 TGGATAAGTT
* *
18765683 GTAGAATTATCGAAATACCCCTGTATG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
18765710 GTAGAATTATCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
***
18765737 GTAGAATTATTAAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
18765764 GTAGAATTACCGAAATACCCCTATAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
18765791 ATAGAATTACCAAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
18765818 GTAGAAATACCGAAATACCCATGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * *
18765845 GTAGAATTACTGAGATACCCTTGTTGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
18765872 GTATAATTACC
1 GTAGAATTACC
18765883 ATTTTTCTCG
Statistics
Matches: 151, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 151 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:18770253 original size:57 final size:57
Alignment explanation
Indices: 18770158--18770515 Score: 527
Period size: 57 Copynumber: 6.2 Consensus size: 57
18770148 GATCTCATTT
* * * *
18770158 CACACACTTAGTGCCCCAACAACCGATCTTGCACACACAGTGCTTGGTTACAGAACTCG
1 CACACAC--AGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
18770217 CACACACAGTGCCTCAACAACTGATCTCGCATACACAGTGCTTGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
18770274 CACACATAGTGCCTCAACAACCAATCTCGCACACACAGTGCTTGGTTACGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * *
18770331 CACACACAGTGCCTCAATAACCGATCTCGCACACACATTGCTCGGTTATGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
*
18770388 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTATGGAACTCG
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
* * * **
18770445 CACACACAGTGCCTCAACAACCAATCTCTCACACACAGTGCTCGATTACGGAACTTA
1 CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
18770502 CACACACAGTGCCT
1 CACACACAGTGCCT
18770516 ATGTTCACTT
Statistics
Matches: 276, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
57 269 0.97
59 7 0.03
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (57 bp):
CACACACAGTGCCTCAACAACCGATCTCGCACACACAGTGCTCGGTTACGGAACTCG
Found at i:18770513 original size:28 final size:28
Alignment explanation
Indices: 18770188--18770513 Score: 224
Period size: 28 Copynumber: 11.5 Consensus size: 28
18770178 AACCGATCTT
* * *
18770188 GCACACACAGTGCTTGGTTACAGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
18770216 GCACACACAGTGCCTCAACAACTGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
* * *
18770245 GCATACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* * ** *
18770273 GCACACATAGTGCCTCAACAAC-CAATCTC
1 GCACACACAGTG-CTCGATTACGGAA-CTC
* *
18770302 GCACACACAGTGCTTGGTTACGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* * * *
18770330 GCACACACAGTGCCTCAATAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
* * *
18770359 GCACACACATTGCTCGGTTATGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** * *
18770387 GCACACACAGTGCCTCAACAACCGATCTC
1 GCACACACAGTG-CTCGATTACGGAACTC
* *
18770416 GCACACACAGTGCTCGGTTATGGAACTC
1 GCACACACAGTGCTCGATTACGGAACTC
* ** *
18770444 GCACACACAGTGCCTCAACAAC-CAATCTC
1 GCACACACAGTG-CTCGATTACGGAA-CTC
* *
18770473 TCACACACAGTGCTCGATTACGGAACTT
1 GCACACACAGTGCTCGATTACGGAACTC
*
18770501 ACACACACAGTGC
1 GCACACACAGTGC
18770514 CTATGTTCAC
Statistics
Matches: 218, Mismatches: 71, Indels: 18
0.71 0.23 0.06
Matches are distributed among these distances:
28 116 0.53
29 102 0.47
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.19
Consensus pattern (28 bp):
GCACACACAGTGCTCGATTACGGAACTC
Found at i:18771031 original size:26 final size:26
Alignment explanation
Indices: 18771002--18771054 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
18770992 ACTTTTCATA
18771002 CACACGTATATTATCCTTTAATCAGG
1 CACACGTATATTATCCTTTAATCAGG
18771028 CACACGTATATTATCCTTTAATCAGG
1 CACACGTATATTATCCTTTAATCAGG
18771054 C
1 C
18771055 TTACAAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (26 bp):
CACACGTATATTATCCTTTAATCAGG
Found at i:18772535 original size:26 final size:26
Alignment explanation
Indices: 18772506--18772565 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
18772496 TCCCTTTGAA
* * *
18772506 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
18772532 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
18772560 CCATTC
1 TCATTC
18772566 TCAATATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:18772551 original size:28 final size:28
Alignment explanation
Indices: 18772520--18772591 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
18772510 TCGATATTTT
*
18772520 GCACACTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
18772548 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
* * *
18772576 GTACACTGAGTACCAT
1 GCACACTAAGTGCCAT
18772592 ATTTGATTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:18779504 original size:20 final size:20
Alignment explanation
Indices: 18779479--18779523 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
18779469 ATGAACTAAA
* *
18779479 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTATAAAATTTG
*
18779499 ATGAAAAATTATAAAATTTT
1 ATGAAAAATTATAAAATTTG
18779519 ATGAA
1 ATGAA
18779524 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTATAAAATTTG
Found at i:18785808 original size:23 final size:23
Alignment explanation
Indices: 18785778--18785824 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
18785768 CAAAGATCAC
18785778 TACTAATAATATGTATACATACA
1 TACTAATAATATGTATACATACA
*
18785801 TACTAATAATATTTATACATACA
1 TACTAATAATATGTATACATACA
18785824 T
1 T
18785825 TTCTTGCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (23 bp):
TACTAATAATATGTATACATACA
Found at i:18786943 original size:43 final size:43
Alignment explanation
Indices: 18786888--18786997 Score: 107
Period size: 45 Copynumber: 2.5 Consensus size: 43
18786878 CGGCATTTTT
* * *
18786888 CCTGCTAGGCTCGAGGCCCGATA-TCAT-TTCACCGGCTTTATAG
1 CCTGCTAAGCTCGAGGCCCGATAGT-ATCTT-ACCGACATTATAG
*
18786931 CCTGCTAAGCTCGAAAGCCCGAATAGTATCTTACCGACATTATAG
1 CCTGCTAAGCTCG-AGGCCCG-ATAGTATCTTACCGACATTATAG
* *
18786976 TCTGCTAAGCTCAAAGGCCCGA
1 CCTGCTAAGCTC-GAGGCCCGA
18786998 ATAATCAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
43 12 0.22
44 7 0.13
45 33 0.60
46 3 0.05
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (43 bp):
CCTGCTAAGCTCGAGGCCCGATAGTATCTTACCGACATTATAG
Found at i:18787384 original size:43 final size:43
Alignment explanation
Indices: 18787335--18787443 Score: 191
Period size: 43 Copynumber: 2.5 Consensus size: 43
18787325 GCATTACGCT
*
18787335 TGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAAGCC
1 TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCC
18787378 TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCC
1 TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCC
* *
18787421 TGCTAGGCATGAAGGCCTGAATA
1 TGCTAGGCACGAAGGCCCGAATA
18787444 TAATACCAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 63 1.00
ACGTcount: A:0.31, C:0.31, G:0.26, T:0.12
Consensus pattern (43 bp):
TGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAAGCC
Found at i:18787484 original size:38 final size:38
Alignment explanation
Indices: 18787441--18787541 Score: 121
Period size: 38 Copynumber: 2.7 Consensus size: 38
18787431 GAAGGCCTGA
** * * * *
18787441 ATATAATACCAGTGCTAGGCCTGCGGGATTTATCCCAG
1 ATATAATACCAGCACGAAGCCTGCGCGATTTAACCCAG
18787479 ATATAATACCAGCACGAAGCCTGCGCGATTTAACCCAG
1 ATATAATACCAGCACGAAGCCTGCGCGATTTAACCCAG
** *
18787517 ATATTTTACCAGCCCGAAGCCTGCG
1 ATATAATACCAGCACGAAGCCTGCG
18787542 GGTCTTTAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (38 bp):
ATATAATACCAGCACGAAGCCTGCGCGATTTAACCCAG
Found at i:18791321 original size:7 final size:7
Alignment explanation
Indices: 18791297--18791337 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
18791287 TAGTCTTAAA
18791297 ATAAAAT
1 ATAAAAT
*
18791304 A-AAAGT
1 ATAAAAT
*
18791310 A-AAAAC
1 ATAAAAT
18791316 ATAAAAT
1 ATAAAAT
18791323 ATAAAAT
1 ATAAAAT
18791330 ATAAAAT
1 ATAAAAT
18791337 A
1 A
18791338 AAAGTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 9 0.31
7 20 0.69
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (7 bp):
ATAAAAT
Found at i:18811170 original size:55 final size:54
Alignment explanation
Indices: 18811111--18811237 Score: 155
Period size: 55 Copynumber: 2.3 Consensus size: 54
18811101 GCAGTGGGCG
* * * * **
18811111 AACCTGCCAAAACAACATGGGCGTGCGACATGCCCGTGCCTGGAAACCGTGGCTA
1 AACCTGCCAAAACAACACGGGCGTGAGACACGCCCATGCCAAGAAACCGTGGC-A
* ** *
18811166 AACCTGTCAAATTAACACGGGCGTGAGACACGCCCATGCCAAGCAACCGTGGCA
1 AACCTGCCAAAACAACACGGGCGTGAGACACGCCCATGCCAAGAAACCGTGGCA
18811220 AACCTGCCAAAACAACAC
1 AACCTGCCAAAACAACAC
18811238 CGACGTGGAC
Statistics
Matches: 59, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
54 16 0.27
55 43 0.73
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.13
Consensus pattern (54 bp):
AACCTGCCAAAACAACACGGGCGTGAGACACGCCCATGCCAAGAAACCGTGGCA
Found at i:18814766 original size:16 final size:16
Alignment explanation
Indices: 18814745--18814775 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
18814735 TAAAATGCTC
18814745 AACTTGGAATGTGTGA
1 AACTTGGAATGTGTGA
18814761 AACTTGGAATGTGTG
1 AACTTGGAATGTGTG
18814776 GGGGTATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.32, T:0.32
Consensus pattern (16 bp):
AACTTGGAATGTGTGA
Found at i:18820601 original size:13 final size:13
Alignment explanation
Indices: 18820583--18820607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18820573 TACCCTATTT
18820583 TCGCACGGTCGTA
1 TCGCACGGTCGTA
18820596 TCGCACGGTCGT
1 TCGCACGGTCGT
18820608 GTTTCCATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.24
Consensus pattern (13 bp):
TCGCACGGTCGTA
Found at i:18828387 original size:49 final size:49
Alignment explanation
Indices: 18828315--18828489 Score: 206
Period size: 49 Copynumber: 3.5 Consensus size: 49
18828305 TGAGGTCACG
* * *
18828315 TGTGTAGTACTAAGTGCAAGCTACTACGTGTACCGGGTAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * * * * *
18828364 TGTGTAGTATTAAGTGTAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-TT-GGTCGCA
*
18828415 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* *
18828464 TGTGTAGTATTATGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
18828490 TGCATACCAG
Statistics
Matches: 103, Mismatches: 21, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
49 60 0.58
50 4 0.04
51 39 0.38
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:18828485 original size:100 final size:100
Alignment explanation
Indices: 18828310--18828502 Score: 314
Period size: 100 Copynumber: 1.9 Consensus size: 100
18828300 TATTGTGAGG
* * *
18828310 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCGGGTAATTGGTCGCATGTGTAGTATT
1 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTATT
* * *
18828375 AAGTGTAGGCTACTATGCGTACCCGATAACTTCGA
66 AAGTGCAGGCTACTATGCATACCAGATAACTTCGA
*
18828410 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTATT
1 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTATT
*
18828475 ATGTGCAGGCTACTATGCATACCAGATA
66 AAGTGCAGGCTACTATGCATACCAGATA
18828503 GCTTTGGATA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 85 1.00
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (100 bp):
TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTATT
AAGTGCAGGCTACTATGCATACCAGATAACTTCGA
Found at i:18828532 original size:100 final size:100
Alignment explanation
Indices: 18828314--18828535 Score: 268
Period size: 100 Copynumber: 2.2 Consensus size: 100
18828304 GTGAGGTCAC
* * * * * *
18828314 GTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCGGGTAATTGGTCGCATGTGTAGTATTAAGT
1 GTGTGTAGAAATAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTATTAAGT
* * * *
18828379 GTAGGCTACTATGCGTACCCGATAACTTCGATCAC
66 GCAGGCTACTATGCATACCAGATAACTTCGATCAA
* * *
18828414 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTATTATGT
1 GTGTGTAGAAATAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTATTAAGT
* *
18828479 GCAGGCTACTATGCATACCAGATAGCTTTGGATACAA
66 GCAGGCTACTATGCATACCAGATAAC-TTCGAT-CAA
*
18828516 GTGTG-A-AAATATGTGCAGGC
1 GTGTGTAGAAATAAGTGCAGGC
18828536 AACTGAGTAT
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
100 93 0.88
101 6 0.06
102 7 0.07
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (100 bp):
GTGTGTAGAAATAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGTGTAGTATTAAGT
GCAGGCTACTATGCATACCAGATAACTTCGATCAA
Found at i:18831457 original size:40 final size:40
Alignment explanation
Indices: 18831413--18831636 Score: 271
Period size: 40 Copynumber: 5.7 Consensus size: 40
18831403 GCTCCTCGTT
* *
18831413 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
18831453 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
18831493 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* *
18831532 CAAATGCCTTC-GGATCTTAGTCCGGAT-TAGTATCTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAACTCGCA
* * * *
18831571 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
18831612 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
18831637 CATCATTCAA
Statistics
Matches: 164, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
38 2 0.01
39 71 0.43
40 80 0.49
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:18831515 original size:79 final size:77
Alignment explanation
Indices: 18831413--18831636 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 77
18831403 GCTCCTCGTT
* *
18831413 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
18831478 ATTTAGTAACTCGCA
64 A-TTAGTAACTCGCA
* * *
18831493 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
*
18831557 ATTAGTATCTCGCA
64 ATTAGTAACTCGCA
* * * * *
18831571 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
18831635 GA
63 GA
18831637 CATCATTCAA
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
78 29 0.23
79 69 0.56
80 26 0.21
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
TAGTAACTCGCA
Found at i:18846548 original size:24 final size:24
Alignment explanation
Indices: 18846478--18846548 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 24
18846468 TAGCTCAAAA
* * * *
18846478 GAGCATCCCGATATTAGCTCTCAT
1 GAGCTTCCCGTTAATAGCTCTTAT
* * *
18846502 GAGCTTCCTGTTTAATGGTTCTTAT
1 GAGCTTCCCG-TTAATAGCTCTTAT
18846527 GAGCTTCCCGTTAATAGCTCTT
1 GAGCTTCCCGTTAATAGCTCTT
18846549 CGGAGCATCC
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (24 bp):
GAGCTTCCCGTTAATAGCTCTTAT
Found at i:18846660 original size:26 final size:24
Alignment explanation
Indices: 18846605--18846672 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 24
18846595 CTTAGCTTTT
18846605 ATGAGCTTCCCGATTATGACTCTTC
1 ATGAGCTTCCC-ATTATGACTCTTC
* *
18846630 ATGAGCTTCCCATTAATTGGCTCTTT
1 ATGAGCTTCCCATT-A-TGACTCTTC
* *
18846656 GTGAGCTTCCCAATATG
1 ATGAGCTTCCCATTATG
18846673 GCTCACTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.14
25 13 0.35
26 19 0.51
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.37
Consensus pattern (24 bp):
ATGAGCTTCCCATTATGACTCTTC
Done.